When using the AIP Backup & Restore tool to restore/replace an Item Object, the Bitstreams (Files) do not currently retain the same Sequence ID (DB column 'sequence_id').
The Sequence ID is often used by the UI to help identify a specific Bitstream/File for download. Although this Identifier is not globally unique, it is unique within a particular Bundle. It's not guaranteed to be "persistent", but it's as close to an "internal persistent ID" as we currently have for a Bitstream/File.
As the Sequence ID is currently stored in an Item AIP, we should make sure to restore it as well. This ensures that previous links/bookmarks to the Bitstream (which may include the Sequence ID) should still function properly after a restore/replace has taken place.
I'll fix this shortly on Trunk, as it's actually a minor code change.