If the domain changes, then you need to add a new managed domain on PGP Universal Server.
To add a new managed domain to PGP Universal server do the following:
Note: If you are using PGP Desktop clients, then you will have to re-enroll all the users for the changes to take affect.
Once the new domain has been added to Managed Domains, you will need to update your hostname (System tab, Network) to reflect the domain change and obtain a new SSL certificate.
If you are only using PGP Whole Disk Encryption, you may want to consider creating a new PGP Universal Server under the new domain, modifying the PGPSTAMP value on the clients, and re-enrolling to the new server. Then you can decommission the old server.