Elasticsearch Snapshot Failing in AWS, preventing upgrade - elasticsearch

Question

My incremental Snapshots in Elasticsearch are now failing. I didn't touch anything, nothing seems to have changed, can't figure out what is wrong.
I checked my Snapshots by doing: GET _cat/snapshots/cs-automated?v&s=id and finding the details of a failed one:
GET _snapshot/cs-automated/adssd....
Which showed this stacktrace:
java.nio.file.NoSuchFileException: Blob object [YI-....] not found: The specified key does not exist. (Service: Amazon S3; Status Code: 404; Error Code: NoSuchKey; Request ID: 21...; S3 Extended Request ID: zh1C6C0eRy....)
at org.elasticsearch.repositories.s3.S3RetryingInputStream.openStream(S3RetryingInputStream.java:92)
at org.elasticsearch.repositories.s3.S3RetryingInputStream.<init>(S3RetryingInputStream.java:72)
at org.elasticsearch.repositories.s3.S3BlobContainer.readBlob(S3BlobContainer.java:100)
at org.elasticsearch.repositories.blobstore.ChecksumBlobStoreFormat.readBlob(ChecksumBlobStoreFormat.java:147)
at org.elasticsearch.repositories.blobstore.ChecksumBlobStoreFormat.read(ChecksumBlobStoreFormat.java:133)
at org.elasticsearch.repositories.blobstore.BlobStoreRepository.buildBlobStoreIndexShardSnapshots(BlobStoreRepository.java:2381)
at org.elasticsearch.repositories.blobstore.BlobStoreRepository.snapshotShard(BlobStoreRepository.java:1851)
at org.elasticsearch.snapshots.SnapshotShardsService.snapshot(SnapshotShardsService.java:505)
at org.elasticsearch.snapshots.SnapshotShardsService.access$600(SnapshotShardsService.java:114)
at org.elasticsearch.snapshots.SnapshotShardsService$1.doRun(SnapshotShardsService.java:386)
at org.elasticsearch.common.util.concurrent.ThreadContext$ContextPreservingAbstractPrioritizedRunnable.doRun(ThreadContext.java:763)
at org.elasticsearch.common.util.concurrent.AbstractRunnable.run(AbstractRunnable.java:37)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
Don't know how to resolve this I can now longer upgrade my index, I checked this page: Resolve snapshot error in .. but still struggling. I've tried deleting a whole bunch of indicies. I may try restoring an old Snapshot. I also delete some .opendis.. indicies used for tracking ILM and a .lock index as well but nothing is helping. Very annoying.
as requested in comments:
GET /_cat/repositories?v
id type
cs-automated s3
GET /_cat/snapshots/cs-automated produces heaps of Snapshots all of which are PARTIAL in their status:
2020-09-08t01-12-44.ea93d140-7dba-4dcc-98b5-180e7b9efbfa PARTIAL 1599527564 01:12:44 1599527577 01:12:57 13.4s 84 177 52 229
2021-02-04t08-55-22.8691e3aa-4127-483d-8400-ce89bbbc7ea4 PARTIAL 1612428922 08:55:22 1612428957 08:55:57 35s 208 793 31 824
2021-02-04t09-55-16.53444082-a47b-4739-8ff9-f51ec038cda9 PARTIAL 1612432516 09:55:16 1612432552 09:55:52 35.6s 208 793 31 824
2021-02-04t10-55-30.6bf0472f-5a6c-4ecf-94ba-a1cf345ee5b9 PARTIAL 1612436130 10:55:30 1612436167 10:56:07 37.6s 208 793 31 824
2021-02-04t11-......

Answer 1

The reason for snapshot to end in PARTIAL state is that because of some issue in S3 repository YI-.... file is missing. Which is clear case of repository corruption.
java.nio.file.NoSuchFileException: Blob object [YI-....] not found:
The specified key does not exist. (Service: Amazon S3; Status Code:
404; Error Code: NoSuchKey; Request ID: 21...; S3 Extended Request ID:
zh1C6C0eRy....)
This kind of repository corruption is observed when cluster is heavily loaded (JVM > 80% or CPU utilization >80%) and few of nodes drops out of cluster.
One way to fix the issue is to delete all the snapshots that refers to index referred by "YI-....". This will cleanup S3 snapshot files of index YI-.... and now when you take new snapshot everything starts afresh.
To be on safer side, I would recommend to contact AWS support to fix this type of repository corruption.
Elasticsearch reference similar issue fixed in elasticsearch version 7.8 and above : https://github.com/elastic/elasticsearch/issues/57198