Just lost most user-installed apps with iPhone 4 sync

I just plugged in my wife's iPhone 4 (iOS 6, Mac OS 10.7.4, iTunes 10 -- not 11 yet!), received a message I've seen before about finding items on the iPhone that weren't on iTunes and did I want to transfer them, and thinking that they were tunes I had deleted on iTunes recently, said no I didn't want to transfer them back to iTunes. (This has happened before and I had to re-delete the stuff I'd deleted from iTunes previously.)
Then the phone synced, and lo and behold, I think every single user-installed app on her phone has disappeared. I can't find any record of them on the Apps tab in iTunes, they're just gone!
After some research that yielded no help, I decided to restore her phone from an earlier backup, but the only backup that was available was not dated, and when I restored the phone to that backup, it was in the same state as before -- no user-installed apps!
Doesn't iTunes store multiple backups from which you can restore your iPhone? Shouldn't I be able to restore her iPhone from say, yesterday's backup and get back all those apps?
She wants my head, mates, and I don't even know *** happened?
Please advise, if you have any...
With thanks,
Dustin
Dartmouth, NS, Canada

You should be able to go to the App Store on her iPhone, click "Updates" in the lower right, then "Purchased" on top, and see all her purchased apps there.  You can restore them from there.

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