rsync with --delete will delete on the destination any files that don't exist on source but IIRC it will leave the empty folders, you can delete those after, if that's OK you can use:
rsync -av --delete /mnt/share/ dest_IP:/mnt/share/
Double check paths are correct before running, or do a dry run.
Another option is to run a sync utility in a Windows PC, like syncbackfree, it will be probably be a little slower but it will also delete the empty folders, or use rsync first then this to delete the empty folders.