Ok, some feedback is due here for anyone else who comes across this thread. As I'd built the mechine using a config backup and restore, it knew my credentials and it self-registered so I did not know what to do. I raised a ticked and basically what Philippe said is more or less right.

As the new system was registered, the first thing I had to do was log into the Clearcenter portal and delete the registration. Then, on the new system, go into Webconfig > System > Settings > System Registration where the system now appears unregistered. You can now register from here registering the system as an Upgrade/Reinstall and select your old system name. Your licences will follow as they stay registered to the system. This did not work with Roundcubemail so I needed a bit more Clearcenter support.

There is a caveat and I quote from their support e-mail:

BTW - this does not work if your old system was on a 6.x Pro and your new system is a 7.x Business...in that case, we need to change your license so that it can register a version 7 box...if that's the case, just let me know.

Nick

If you register your new server at clear, the old server will unregister and visaversa

Do I have to delete or rename a system on my ClearCenter account then rename the other machine?

I have not done this in a while, in the old days you would register the new system by reusing the existing Service Name from the ClearCenter list, this would automatically remove the registration associated to the server (I believe the suva service?). After that if needed you could always register the old server to a new name.

In regards to the subscription, not sure, I think it follows the Service Name.