We are running an ePO 4.6 server managing agents in three AD domains. We are planning to add a new AD domain tree with a limited number of systems in it, which will need to have some of the same computer names (NETBIOS) as our primary domain, but of course with the new domain suffix. So for example most of our machines are in Contoso.com, but the new domain will be Fabrikam.com and will contain some systems with the same names that live in Contoso.com. So there might be a system named MyEndpoint.Contoso.com, and the new domain will have a MyEndpoint.Frabrikam.com. These will have different MAC addresses, different IP addresses, and separate agent installations on them. We will not be using encryption on any of these systems, and we do not use Active directory to synchronize new systems at all.
My understanding is that a new GUID would be generated on these new Fabrikam.com systems, so ePO would track both of the systems with the name "MyEndpoint" and treat them both as valid, separate, managed systems. They are separate in every way except for the NETBIOS name, and that is why we have them in separate domain trees. Am I missing any potential issues with this scenario, or will this work as I am thinking it will?
As long as the GUID is unique you should be fine. I have several systems in my 4.5 environment that have the same hostname and different GUIDS and they update and report in without issue.