|If this is indeed an Active Directory domain then all domain PC's will need to contact the DC in order to be authenticated. From the sounds of it, you have two domains and some clients are connecting to the old, others the new.|
I suspect you're going to have to go around machine by machine and remove the ones still attached to the old domain from it, and then join them to the new domain. Although you could probably just shut the DC(s) down for the old domain and wait for users to call you when they can't login.
This is the wrong place for this post, it should be in one of the "Windows Server" forums, but I'm not moving it as I find I'm quite interested in what's going on here.
It's been a while since I did any domain admin duties so my MS and AD skills are rusting. But, we do have some guys who do this day in and day out that hang in this particular forum and hopefully, they'll jump in with some suggestions.
It matters not how straight the gate,
How charged with punishments the scroll,
I am the master of my fate;
I am the captain of my soul.