Spring Integration: Inbound File Adapter drops files when service restarts

Question

We're using the S3InboundFileSynchronizingMessageSource feature of Spring Integration to locally sync and then send messages for any files retrieved from an S3 bucket.

Before syncing, we apply a couple of S3PersistentAcceptOnceFileListFilter filters (to check the file's TimeModified and Hash/ETag) to make sure we only sync "new" files.

Note: We use the JdbcMetadataStore table to persist the record of the files that have previously made it through the filters (using a different REGION for each filter).

Finally, for the S3InboundFileSynchronizingMessageSource local filter, we have a S3PersistentAcceptOnceFileListFilter FileSystemPersistentAcceptOnceFileListFilter -- again on TimeModified and again persisted but in a different region.

The issue is: if the service is restarted after the file has made it through the 1st filter but before the message source successfully sent the message along, we essentially drop the file and never actually process it.

What are we doing wrong? How can we avoid this "dropped file" issue?