I don't know what to do in this situation but I would prefer deleting Bonjour, Apple Application Support & Apple Software Update folders from Program Files... Using a Registry Cleaner & clean the Registry... This will delete Registry Entries such as Missing Shared dlls, Unused File Extensions, ActiveX and Class Issues, etc. The Best Registry Cleaners Available in Market are Ace Utilities, Advanced Registry Optimizer, C-Cleaner, Glary Utilities, Reg Organizer, Registry Life, Registry Mechanic, Tune Up Utilities 2010, WinUtilities, Wise Registry Cleaner Pro, Wonder-Share Registry Optimizer... Since, the process removes only unused files, the files required for working of iTunes will not be deleted from the registry...