I use rsync for backups. If you use the right options I think it can do
what you are asking for eg.

rsync -tr --delete source destination

copies all files and directories the first time you use the command.
Next time it will only copy new and changed files. Furthermore it will
delete files from dest which no longer exist on the source. There's a
graphical interface for rsync - grsync - which is also in synaptic. Hope
this helps.

Oh, and by the way, the upgrade to 8.04 went smooth, no problems, the
only thing I miss is xmms like a few others.