My iTunes likes to periodically delete all my applications. I caught it 'syncing' my apps again today. Only a few apps were deleted, but I'd like to know which ones. Does iTunes store sync changes in a log file?
Per Apple Tech Support Senior iPhone Technician Christina, whom I just had the pleasure of working with (1/3/12 @ ~9:05am Central Time), iTunes does NOT keep any type of "log" file that can be located & viewed to assist you with troubleshooting.
Her suggestion was to use the "msinfo32" command (from either a DOS prompt, or the START-->SEARCH feature in Windows 7, you will also most likely need Administrator rights, but have not tested this to confirm) and then "dig through" the information.