Client has two domains and wants there only to be one. Domain A's DC is an sbs2k machine, and Domain B's is a 2k3 running at Windows 2000 Mixed functional level. Along with changing the domain name I will need to change the computer name as it is identical to one already on domain A. I read that it's required to change 2k3's functional level to 2003 in order to make name changes changes using netdom. So I believe I'm unable to carry out task without a clean install. What can I do?
I would suggest your best option is to demote the DC in domain B, rename it, join it to domain A and then promote it to being a DC in domain A.
Otherwise, even if you are able to change the name, you are still going to have issues with that machine being a DC in domain B. Do it properly first time and you will have less issues in the long term.