It is amazing the things you see flying by in an rsync.. Cant count the number of times I've halted the process, deleted the offending kruft, and then started again.

rsync need a magic –no-kruft option that will (somehow) magically parse what is no longer needed or wanted and just leave it behind. or with the –KILL-KRUFT option (caps to prevent accidental use) delete the offending kruft from the source as it is archiving it.