Itunes update deleted my backups

My BOSS updated his iphone 4 to iOS5 and his itunes software this morning on his windows7pro PC. Now all of his apps are gone.
He still has his contacts, thank god.
Additionally when I looked in his profile under AppData\Roaming\Apple Computer\MobileSync\Backup, there is only one backup file and it is from today. We've backed up his phone several times on this machine.
WHERE DID THE BACKUPS GO???? Where did his apps go????
This is very frustrating because it's not the first we've lost data during updates.
Apple seems to treat users data as a secondary concern.
I have advised all of my iphone holding users to not upgrade to the new iOS until this is resolved.

Same happened to me Yesterday. I updated my itunesand  upgraded my iPad OS to iOS 5.01 and all my backups gone. This is too much. Apple must consider this seriously. If you found any solution please tell me. It's really frustrating.

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