Letsencrypt script pointed to incorrect hostname

If you check letsencrypt.sh you can see it determines if it is a request for the server hostname like this:
1. The domain must not be in /etc/virtual/domainowners
2. The domain must be in /etc/virtual/domains
3. The output of "/usr/local/directadmin/directadmin c | grep serveame" must match the domain you are requesting it for.

if the certificate you are requesting matches this it'll be treated as a cert for the hostname.

The letsencrypt.sh script will create the san config if it does not yet exist, so you should be able to move it just fine and then request the cert, granted other conditions are met. It's simply re-using the existing SAN, but removing (or editing) it shouldn't matter.