The empegClone utility does a complete copy. Not sure about jEmplode.
More to the point, empegClone only works over USB, and only works from lower serial numbers to higher.

There's two different ways to do it listed at my website: netcat and rsync. The first also does a complete copy, but is a darn sight quicker than empegClone. The second does a proper synchronisation, and is very quick. I use it maybe two or three times a week.