Rsync has a possibility to delete the to-be-deleted files in the destination before it starts syncing files that actually need syncing. That is sorely missing in Shirt Pocket's program SuperDuper!, which is actually a nice backup program, and for some time was one of the few sane options available to make fully reliable backups. SuperDuper! just starts copying blindly, and can then find itself in the situation where the backup destination can't contain the new files + the old files that should be deleted but still weren't. So that problem would be solved with rsync's "delete first" behaviour. I see there have been people complaining about this in Shirt Pocket's forums for at least 5 years, and the developers seem to only say "yes, we will do something sometime". But they still didn't. So, this is the command line to be used: sudo rsync --delete --existing --ignore-existing --recursive /Volumes/ORIGINAL_VOLUME/ /Volumes/BACKUP_VOLUM...