Just updated to iOS5 yesterday and today noticed a couple apps lost all data. I did back up everything prior to update. Will a restore bring data back to these apps?
It should. Wipe and restore it again.
Sucks that something went wrong for you, but it should all still be in the backup so a re-do will hopefully fix it.
Word of advice: Let it completely finish on its own. I've seen instances where is SAYS it did apps and is now doing music, but where canceling the "music" syncing left several apps un-finished.
I think that top bar in iTunes that says what it's currently doing isn't always accurate. Let the whole thing finish before you eject it.