How about if you move all of your iPhone backups out of the mobile sync folder, and then just make a new backup for the phone from the way it is. Control click on the phone and go to backup.

Quit iTunes before moving anything around.

You may need to de-authorize all your devices, then reauthorize them.

Just a few things off the top of my head, not at home, on the phone. Make sure you backup all those mobile sync files before you move them out of the folder.