How does the risk of inconsitency really affect the site.
Option 1): There is a file backed up whose revision_id in the database has not been recorded. You loose the file, but have it on disk lingering around and it might be restored.
Option 2): There is a file recorded in the database, but it is no longer there. In this case you can ask the users to upload their files again (wording: "If you uploaded the file within the last @backup_interval@, please revisit our site as it might have been lost").