I found all the apps exactly where they are supposed to be (iTunes/iTunes Media/Mobile Applications) but nothing I did would make itunes find them. Then I decided to be silly and just drag and drop them into the apps screen - and now they are all there.

So weird that it didn't find them itself.

This was for a new iPod Touch on 4.1, so the firmware can't be the issue. I'm wondering whether this was a bug in iTunes 10?

Anyway, they all appear to be moving back (all 240 of them)

Thanks!