diff --git a/CHANGELOG.md b/CHANGELOG.md
index a917705dd72..b043edcb6bc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -110,6 +110,7 @@ We use *breaking :warning:* to mark changes that are not backward compatible (re
 - [#6592](https://github.com/thanos-io/thanos/pull/6592) Query Frontend: fix bugs in vertical sharding `without` and `union` function to allow more queries to be shardable.
 - [#6317](https://github.com/thanos-io/thanos/pull/6317) *: Fix internal label deduplication bug, by resorting store response set.
 - [#6189](https://github.com/thanos-io/thanos/pull/6189) Rule: Fix panic when calling API `/api/v1/rules?type=alert`.
+- [#6598](https://github.com/thanos-io/thanos/pull/6598) compact: fix data corruption with "invalid size" error during downsample
 
 ### Changed
 - [#6049](https://github.com/thanos-io/thanos/pull/6049) Compact: *breaking :warning:* Replace group with resolution in compact metrics to avoid cardinality explosion on compact metrics for large numbers of groups.
diff --git a/pkg/compact/downsample/downsample.go b/pkg/compact/downsample/downsample.go
index 78b615f9047..51d895058ac 100644
--- a/pkg/compact/downsample/downsample.go
+++ b/pkg/compact/downsample/downsample.go
@@ -372,8 +372,17 @@ func downsampleRawLoop(data []sample, resolution int64, numChunks int) []chunks.
 		for ; j < len(data) && data[j].t <= curW; j++ {
 		}
 
-		batch := data[:j]
+		batch := make([]sample, 0, j)
+		for _, s := range data[:j] {
+			if math.IsNaN(s.v) {
+				continue
+			}
+			batch = append(batch, s)
+		}
 		data = data[j:]
+		if len(batch) == 0 {
+			continue
+		}
 
 		ab := newAggrChunkBuilder()
 
diff --git a/pkg/compact/downsample/downsample_test.go b/pkg/compact/downsample/downsample_test.go
index d1dfaeb9b8e..16cc9246172 100644
--- a/pkg/compact/downsample/downsample_test.go
+++ b/pkg/compact/downsample/downsample_test.go
@@ -34,6 +34,686 @@ func TestMain(m *testing.M) {
 	goleak.VerifyTestMain(m)
 }
 
+func TestDownsampleAndReadResultingData(t *testing.T) {
+	data := []sample{
+		{t: 1688526018213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526078213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688526138213, v: math.Float64frombits(4607156757263679111)},
+		{t: 1688526198213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526258213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526318213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526438213, v: math.Float64frombits(4607105434191002523)},
+		{t: 1688526498213, v: math.Float64frombits(4607143926495509974)},
+		{t: 1688526558213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526618213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526678213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526738213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526798213, v: math.Float64frombits(4607131022513257114)},
+		{t: 1688526858213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526918213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688526978213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527038213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527098213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527158213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527218213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527278213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527338213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527398213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527458213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688527518213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527578213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527638213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527698213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527758213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527818213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688527878213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527938213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688527998213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528058213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528118213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528178213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528238213, v: math.Float64frombits(4607092603422833380)},
+		{t: 1688528298213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528358213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528418213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528478213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528538213, v: math.Float64frombits(4607118264959171663)},
+		{t: 1688528598213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528658213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528718213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528778213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528838213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688528898213, v: math.Float64frombits(4607131022513257122)},
+		{t: 1688528958213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529018213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529078213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529138213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529198213, v: math.Float64frombits(4607118264959171672)},
+		{t: 1688529258213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529318213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529378213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529438213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529498213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529558213, v: math.Float64frombits(4607169588031848265)},
+		{t: 1688529618213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529678213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529738213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529798213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529858213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688529918213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688529978213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530038213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530098213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530158213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530218213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530278213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530338213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530398213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530458213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530518213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530578213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530638213, v: math.Float64frombits(4607143926495509973)},
+		{t: 1688530698213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530758213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530818213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530878213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688530938213, v: math.Float64frombits(4607118264959171663)},
+		{t: 1688530998213, v: math.Float64frombits(4607143926495509974)},
+		{t: 1688531058213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531118213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531178213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531238213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531298213, v: math.Float64frombits(4607156757263679111)},
+		{t: 1688531358213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531418213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531478213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531538213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531598213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531718213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531778213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531838213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531898213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688531958213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532018213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688532078213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532198213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532258213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532318213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532378213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532438213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532498213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532558213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532618213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532678213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688532738213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688532798213, v: math.Float64frombits(4607143871584947194)},
+		{t: 1688532858213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688532918213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688532978213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688533038213, v: math.Float64frombits(4607143871584947189)},
+		{t: 1688533098213, v: math.Float64frombits(4607131022513257122)},
+		{t: 1688533158213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533218213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533278213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533338213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533398213, v: math.Float64frombits(4607143926495509968)},
+		{t: 1688533458213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533518213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533578213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533638213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533698213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533758213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533818213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533878213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533938213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688533998213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688534058213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688534118213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688534178213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688534238213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688534298213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688534358213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688534418213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688534478213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688534538213, v: math.Float64frombits(4607131022513257117)},
+		{t: 1688534598213, v: math.Float64frombits(4607156720656637259)},
+		{t: 1688534658213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688534718213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688534778213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688534838213, v: math.Float64frombits(4607105214234976770)},
+		{t: 1688534898213, v: math.Float64frombits(4607156720656637259)},
+		{t: 1688534958213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688535018213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688535078213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688535138213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688535198213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688535258213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688535318213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688535378213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688535438213, v: math.Float64frombits(4607131095727340818)},
+		{t: 1688535498213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688535558213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688535618213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688535678213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688535738213, v: math.Float64frombits(4607156720656637259)},
+		{t: 1688535798213, v: math.Float64frombits(4607143926495509973)},
+		{t: 1688535858213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688535918213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688535978213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536038213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536098213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536158213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688536218213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536278213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536338213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536398213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536458213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536518213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536578213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536638213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536698213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536758213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536818213, v: math.Float64frombits(4607169588031848266)},
+		{t: 1688536878213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536938213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688536998213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537058213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537118213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537178213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688537238213, v: math.Float64frombits(4607131095727340818)},
+		{t: 1688537298213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537358213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537418213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537478213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537538213, v: math.Float64frombits(4607079772654664231)},
+		{t: 1688537598213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537658213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537718213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537838213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688537898213, v: math.Float64frombits(4607079772654664232)},
+		{t: 1688537958213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538018213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538078213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538138213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538198213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538258213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538318213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538378213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538438213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538498213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538558213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538618213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538678213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538738213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538798213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538858213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688538918213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688538978213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688539038213, v: math.Float64frombits(4607118173441567050)},
+		{t: 1688539098213, v: math.Float64frombits(4607131022513257121)},
+		{t: 1688539158213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688539218213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688539278213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688539338213, v: math.Float64frombits(4607143871584947195)},
+		{t: 1688539398213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688539458213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688539518213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688539578213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688539638213, v: math.Float64frombits(4607105434191002518)},
+		{t: 1688539758213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688539818213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688539878213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688539938213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688539998213, v: math.Float64frombits(4607118264959171665)},
+		{t: 1688540058213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540118213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540178213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540238213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540298213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540358213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540418213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540478213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540538213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540598213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540658213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688540718213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688540778213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688540838213, v: math.Float64frombits(4607002531796356391)},
+		{t: 1688540898213, v: math.Float64frombits(4607066611952456451)},
+		{t: 1688540958213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688541018213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688541078213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688541138213, v: math.Float64frombits(value.NormalNaN)},
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+		{t: 1688557698213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688557758213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688557818213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688557878213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688557938213, v: math.Float64frombits(4607092603422833381)},
+		{t: 1688557998213, v: math.Float64frombits(4607079918666250794)},
+		{t: 1688558058213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558118213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558178213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558238213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558298213, v: math.Float64frombits(4607092475298186899)},
+		{t: 1688558358213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558418213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558478213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558538213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558598213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558658213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558718213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558778213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558838213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558898213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688558958213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688559018213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559138213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559198213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559258213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559318213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688559378213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559438213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559498213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559558213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559618213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559678213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688559738213, v: math.Float64frombits(4607105543699692438)},
+		{t: 1688559798213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559858213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559918213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688559978213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560038213, v: math.Float64frombits(4607054293632809136)},
+		{t: 1688560098213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560158213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560218213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560278213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560338213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560398213, v: math.Float64frombits(4607092731182971621)},
+		{t: 1688560458213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560518213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560578213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560638213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560698213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560758213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560818213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560878213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560938213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688560998213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561058213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561118213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561178213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561238213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561298213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561358213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561418213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688561478213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561538213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561598213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561658213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561718213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561778213, v: math.Float64frombits(4607182418800017408)},
+		{t: 1688561838213, v: math.Float64frombits(4607092731182971626)},
+		{t: 1688561898213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688561958213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688562018213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688562078213, v: math.Float64frombits(value.NormalNaN)},
+		{t: 1688562138213, v: math.Float64frombits(4607028449581987651)},
+		{t: 1688562198213, v: math.Float64frombits(4607028668599367493)},
+		{t: 1688562258213, v: math.Float64frombits(value.NormalNaN)},
+	}
+
+	var (
+		reuseIt    chunkenc.Iterator
+		all        []sample
+		aggrChunks []*AggrChunk
+	)
+
+	// downsample from raw to 300s
+	chks := DownsampleRaw(data, ResLevel1)
+	testutil.Assert(t, chks != nil, "Downsample from raw to 300s")
+
+	for _, c := range chks {
+		ac, ok := c.Chunk.(*AggrChunk)
+		if !ok {
+			if c.Chunk.NumSamples() == 0 {
+				continue
+			} else {
+				testutil.Ok(t, expandChunkIterator(c.Chunk.Iterator(reuseIt), &all), "expand chunk %d", c.Ref)
+				aggrDataChunks := DownsampleRaw(all, ResLevel1)
+				for _, cn := range aggrDataChunks {
+					ac, ok = cn.Chunk.(*AggrChunk)
+					testutil.Assert(t, ok, "Not able to convert non-empty XOR chunks to 5m downsampled aggregated chunks.")
+				}
+			}
+		}
+		aggrChunks = append(aggrChunks, ac)
+	}
+
+	// validate aggrChunks from first downsample iteration
+	validateAggrChunks(t, aggrChunks, chks, "First downsample iteration")
+
+	// downsample from 300s to 3600s
+	downsampledChunks, err := downsampleAggr(
+		aggrChunks,
+		&all,
+		chks[0].MinTime,
+		chks[len(chks)-1].MaxTime,
+		ResLevel1,
+		ResLevel2,
+	)
+	testutil.Ok(t, err, "Downsample from 300s to 3600s")
+	testutil.Assert(t, downsampledChunks != nil)
+
+	aggrChunks = aggrChunks[:0]
+	for _, c := range downsampledChunks {
+		ac, ok := c.Chunk.(*AggrChunk)
+		if !ok {
+			if c.Chunk.NumSamples() == 0 {
+				continue
+			} else {
+				t.Fatalf("expected downsampled chunk (*downsample.AggrChunk) got a non-empty %T instead", c.Chunk)
+			}
+		}
+		aggrChunks = append(aggrChunks, ac)
+	}
+
+	// validate arrgChunks from second downsample iteration
+	validateAggrChunks(t, aggrChunks, chks, "Second downsample iteration")
+}
+
+func validateAggrChunks(t *testing.T, aggrChunks []*AggrChunk, chks []chunks.Meta, d string) {
+	for j, c := range aggrChunks {
+		var iters [2]chunkenc.Iterator
+		// we need only 0th and 1st AggrType for alignment check,
+		// but we iterate through all 5 to catch error "invalid size"
+		for i := 0; i < 5; i++ {
+			ac, err := c.Get(AggrType(i))
+			testutil.Ok(t, err, "%s. Get AggrType(%d) from aggrChunk #%d. MinT %d, MaxT %d", d, i, j, chks[j].MinTime, chks[j].MaxTime)
+			if i < 2 {
+				iters[i] = ac.Iterator(nil)
+			}
+		}
+
+		// create iterator to check samples
+		ai := NewAverageChunkIterator(iters[0], iters[1])
+		// exhaust iterator and...
+		for ai.Next() != chunkenc.ValNone {
+		}
+		// ...check its error
+		err := ai.Err()
+		testutil.Ok(t, err, d)
+	}
+}
+
 func TestDownsampleCounterBoundaryReset(t *testing.T) {
 	toAggrChunks := func(t *testing.T, cm []chunks.Meta) (res []*AggrChunk) {
 		for i := range cm {
@@ -282,6 +962,25 @@ func TestDownsample(t *testing.T) {
 
 			expected: realisticChkDataWithCounterResetRes5m,
 		},
+		{
+			name: "three chunks, the first one with NaN values only",
+			inRaw: [][]sample{
+				{{20, math.Float64frombits(value.NormalNaN)}, {40, math.Float64frombits(value.NormalNaN)}, {60, math.Float64frombits(value.NormalNaN)}, {80, math.Float64frombits(value.NormalNaN)}, {100, math.NaN()}, {101, math.Float64frombits(value.StaleNaN)}, {120, math.Float64frombits(value.NormalNaN)}, {180, math.Float64frombits(value.NormalNaN)}, {250, math.Float64frombits(value.NormalNaN)}},
+				{{260, 1}, {300, 10}, {340, 15}, {380, 25}, {420, 35}},
+				{{460, math.Float64frombits(value.StaleNaN)}, {500, 10}, {540, 3}},
+			},
+			resolution: 100,
+
+			expected: []map[AggrType][]sample{
+				{
+					AggrCount:   {{t: 299, v: 1}, {t: 399, v: 3}, {t: 499, v: 1}, {t: 540, v: 2}},
+					AggrSum:     {{t: 299, v: 1}, {t: 399, v: 50}, {t: 499, v: 35}, {t: 540, v: 13}},
+					AggrMin:     {{t: 299, v: 1}, {t: 399, v: 10}, {t: 499, v: 35}, {t: 540, v: 3}},
+					AggrMax:     {{t: 299, v: 1}, {t: 399, v: 25}, {t: 499, v: 35}, {t: 540, v: 10}},
+					AggrCounter: {{t: 260, v: 1}, {t: 299, v: 1}, {t: 399, v: 25}, {t: 499, v: 35}, {t: 540, v: 48}, {t: 540, v: 3}},
+				},
+			},
+		},
 		// Aggregated -> Downsampled Aggregated.
 		{
 			name: "single aggregated chunks",