I have a folder a/ and a remote folder A/. I now run something like this on a Makefile:
get-music: rsync -avzru server:/media/10001/music/ /media/Incoming/music
You might use Osync: http://www.netpower.fr/osync , which is rsync based with intelligent deletion propagation. it has also multiple options like resuming a halted execution, soft deletion, and time control.