I have hard drive that I back up with rsync to a network-attached storage. There are some non-empty directories at the destination (the nas) that do not exist on the source anymore. It is not a permission issue.
I had a mount issue on the OS.
The --delete option does work. The --force option (without the --delete) does not report any more diretory deletions (--progress option).
rsync -raz --progress --delete --ignore-errors --exclude-from='exclude_list.txt' {source} {destination}