Bedrock - Sync error due to file being partially indexed even after deletion of file.

When you're experiencing issues with a Bedrock Knowledge Base sync showing "PARTIALLY_INDEXED" status for a file that you've already deleted from S3, this indicates a synchronization issue between your S3 bucket and the knowledge base.

The "PARTIALLY_INDEXED" status means that some chunks of the document were successfully indexed while others failed. This can happen when there are inconsistencies between the previous version of the file and the current state of your S3 bucket.

Here are some steps to resolve this issue:

1. Understand the incremental syncing process: Bedrock implements incremental syncing, which means it only processes files that have been added, modified, or deleted since the last sync. When files are overwritten (rather than deleted and re-uploaded), this can sometimes cause issues if the number of chunks differs between versions.

2. Check CloudWatch logs: Review the CloudWatch logs for your knowledge base to see the specific error messages related to the failed sync. This might provide more details about why the file is still showing as "PARTIALLY_INDEXED" despite being deleted.

3. Try a complete resync: Instead of an incremental sync, you might need to perform a complete resync of your knowledge base. This can be done by:

• Temporarily moving all files out of the S3 bucket
• Triggering a sync (which should remove all documents)
• Moving the files back (excluding the problematic one)
• Triggering another sync

4. Check for metadata inconsistencies: If you were using metadata files with your documents, ensure that all associated metadata files are also properly deleted.

5. Verify permissions: Ensure that the IAM role associated with your knowledge base has all the necessary permissions for S3 operations, including delete operations.

6. Consider recreating the knowledge base: If all else fails, you might need to create a new knowledge base with the same configuration and data source, which would start with a clean slate.

The issue you're experiencing is likely related to how Bedrock tracks document versions and changes. When files are overwritten rather than deleted and re-uploaded, the system sometimes has difficulty reconciling the differences, especially if the chunking of the document changes.
Sources
AWS Bedrock Knowledge Base not syncing when files are being over-written in S3 Bucket | AWS re:Post
Incremental Syncing of Metadata files | AWS re:Post
KnowledgeBaseDocumentDetail - Amazon Bedrock