Is the XBMC build you are running before your recent upgrade and after the same?
If it's not too much trouble, you may just delete your local database file and have your ATV rescrape everything again?
If you'd like, you can do an export of your database first. Then delete your database. Then reimport the backed up database. Just make sure that any WinSCP or SSH you do related to the path: /var/mobile/Library/Preferences/XBMC should be done with the mobile user. That's because XBMC and all AppleTV apps run as that user, and they will need read/write permissions.
I wrote a post once on the best practice of creating two login profile and using the appropriate one depending on what you intend on editing once you log into your ATV2. Look for that if you want more info.
Anyways, those are some additional things to try if you don't want to start completely from scratch.
Good luck.
-dazex