As many Admins are using rsync for /home, they might be excluding the "Domains Directory" option from their backups. During the restore, DA would try and re-create the subdomains, but because /home/user/domains won't exist, the creation of the subdomain fails, so isn't added to the subdomains list. Fix is to check if "domains" exists in the backup/backup_options.list. If it's not in the list, then we set subdomain creation to skip creation of the path/template, etc.. The subdomain can then be correctly added to the data/users/domains/domain.com.subdomains, so it's added to the apache VirtualHosts. Note, you must still restore /home/user/domains via your manual method, or else you'll obviously have a website that doesn't work, and Apache might not be too happy about it.