There were some reported non-functioning --delete flag when using rsync in syncronizing two filesystems/locations. This may occur due to failures or errors during rsync tries to sync zero size files. One simple work around for this is using --ignore-errors flag. Some examples for taking backup of user directory:
rsync -vaz -e ssh --delete --ignore-errors user@host:/home/user/ local_dir/
rsync -vaz --delete --ignore-errors /home/user/ /media/disk/backup_dir/
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