ITunes deleted apps from my touch

Coincidental or not, before syncing my touch I upgraded the OS to 3.1.1.
Previously my iTunes wasn't backing up my apps; my touch is a couple weeks old, and I hadn't set up iTunes to do so. Tonight I set up iTunes to back up the apps. When I synced, there was a message saying something to the effect of "There are apps on your touch that are not in iTunes. Do you want to copy them to iTunes?" I agreed, and then they were deleted from the touch.
The apps appeared in iTunes, but when I tried to restore them back to the touch, they were all deleted from iTunes.
Has anyone else had an experience like this?

Obviously, restoring from a backup is your first option.
Otherwise, it sounds like - or at least it's possible - that you may have accidentally made two accounts.
If the aforementioned doesn't work, try logging onto iTunes, and then log onto your iTunes Store. The pulldown will have a field for entering your item's email address. Try using another iTunes email address and see what happens.
If this doesn't work, I'd try another approach. First, redownload any free apps. Second, go to Your home/Library/Music/iTunes/Mobile Applications. In Mobile Applications, you should find an archive of your Apps. Drag copies of the Apps you need onto the iTunes/Applications window. Now, sync your unit.

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