You need to make sure you reload your project if it is displayed as out of sync.
See "How to handle project out of sync".
the right answer is to re-load, with the "reload projects out of sync" action. In my experience, this will never overwrite any of your local changes, and it definitely will not change the date stamp on any file that is currently loaded and in-sync with what is in the repository.
(Still, save your local work just in case)