I had this same issue but I'm relieved to say everything worked out for me. I had reformatted my hard drive and reinstalled vista. Of course, before reformatting I made sure to backup all of my iTunes info that was in my user folder. After reinstalling iTunes, I copied that info back into my user directory. Still, when I plugged in my iPhone to sync, I got the message that it would be wiped clean before it would be synced. After downloading iFunBox (which is a neat application but doesn't actually solve this problem) and procrastinating for several days, I finally said the hell with it and pressed the sync button in iTunes, deciding that I'd have to start from scratch. To my great relief, I got a message in iTunes that said I needed to authorize my computer and when I clicked OK, I got another message saying the computer was already authorized. My iPhone synced normally and all of my apps and info were intact. Hopefully this is the case for others and some anxiety is avoided.

Cheers!