As a troubleshooting technique only -- go to System Preferences > MobileMe > Sync and set the sync interval to 1 hour, or more. Then when you notice the deletion you should have plenty of time to go back and check the other sources.
Later on, after resolving the problem, you can go back and reset the sync interval to "automatic".
If we knew what it was we were doing, it wouldn't be called research, would it?
