Ah. Yes, I recommend no restores at all. Pain in the butt I know, but it's the best way to go about that kind of update to ensure you don't have any apps going all wonky. What I do under those circumstances is completely move (not copy) the entire TiBu folder over to my pc and begin an entire new set of backups after the flash.
One free app that I do use for backing up just the apps themselves (no settings whatsoever) is
Android Assistant by Aaron. Under the tools menu is an option called App Backup and Restore. I put a tick in the box for all 3rd party apps (3rd party being apps that did not come with the phone) and back those up. After I flash, I download ES File Explorer, enable Unknown Sources in ANdroid settings (allows you to install apps from your SD), and then proceed to install my apps. After that I check for updates for those apps, then proceed to customize things to my liking.