You will not delete any files when you sync unless Sync Center tries to sync with a file that has been deleted. If you have set up a sync partnership to sync files in two locations (such as between a mobile device and a computer), Sync Center will keep an identical set of files in both locations. If you add or update a file in one location, Sync Center also will add or update it in the other location. Likewise, if you delete a file in one location, Sync Center will delete it from the other location.
If you want to avoid deleting a file when you sync, don't delete it from any of the locations you sync with and the file will be safe. If you are concerned, make a copy of the file and store it in a folder or other location that you are not going to sync with.