the sync happens between the on disk project and the associated nsf. If the view (for example) has been removed from the nsf, it will also be out of the on disk project. As you discovered, adding a backup version to the on disk project returned the view to the nsf. Had you used an Eclipse import rather than a file system copy, you would not have needed the refresh for Eclipse to see it.
So I don't see where a normal sync fits in here if you are in a restore situation?