I don't believe that changing the domain name or PDC Netbios name will cause you any issues, since these are not names that are identified in JDE.
However, you need to be careful with any ACCOUNT NAMES for any of the windows services - for example, the JDE network and queue services. If you are changing the domain name, you need to be careful there.
I do not believe that windows terminal servers will have issues being migrated from one domain to another with the JDE licensing - only if the name of the server changes will you have issues with the license file.
Lastly - watch out for printers ! If you are changing the netbios name of your PDC - is that also the name of your print server ? If so, you need to update your printer definitions in JDE !