If you do an incremental backup of that directory, it should catch the latest changes.
But if you are trying to organize MySQL backups, why not take a look at ZRM (Zmanda Recovery Manager) for MySQL? It manages all the dumps for you, and can do incremental as well as full, tracking everything and giving you an easy management interface. You can still use whatever general backup tool you want to put those on tape, cycle them out to network storage, or whatever. I happen to use Amanda for that, but you don't have to.