A standard sync will theoretically have the same effect (making the target DB match the source). This is the same as clearing down everything from the target then syncing. So I think I'm perhaps missing the point of what you're trying to do.
There's no option in SQL Compare to do this; but a workaround would be to have an empty database on your server, and first sync from this to the target (which should drop everything) then run your usual sync afterwards. But as I said above, the end result would be the same as the sync you're already doing.