He fixed it then
... Sorry, hmm...
I don't know. I've never had that happen to me while scanning a standard MP3 player, my Creative for instance.
I wouldn't have thought it does anything to the drive at all, except scan.
It could have removed files though from the device, but I wouldn't have thought that Microsoft's scanner would have found tempory files from Apple's.
Has Vista by any chance got a backup of what it deletes on the program so you can restore it back?