I get what you mean, I have seen this happen when a windows 200 server was upgraded to 2003. A new domain was created but the server's name remained the same. There for it could never demote the server to remove the old domain information. check this out:
http://www.petri.co.il/delete_failed_dcs_from_ad.htm

I would avoid doing any major demotions or cleaning of metadata until you have some more time to investigate.