This is the story that how ISPConfig has messed up itself: Going into Sites -> Backup stats -> and clicking on a site that is a Vhost Subdomain. You are redirected to the backup tab of a website, Vhost subdomain doesn't have the backup tab, very odd, I thought, so I've changed tab to see if is the right domain, and it saved the configuration and put in queue for apply changes. When it has finished, the vhost subdomain has become magically a full website, with all others subdomains of the main domain. Obviously, the path have changed, and the sites files are gone, deleted. Apache founds an error in the new configuration, so it doesn't start, because the old certificate of a subdomain in not in the folder pointed by the new configuration. At this point, I had to move all the non-working configurations manually, restart apache so I could finally reconnect to ISPConfig. I've removed all the subdomains that has become website, and I tryed to restore a backup in the website father, but it did not work. At this point again, I've deleted the father domain, and recreated all website and subdomain vhost, entirely.