If you need to remove references to orphan domain, you will need to do it by removing naming contexts
Since W2008 versions do not have the “domain management” command, you will need to use the following procedure:
Click Start, click Run, type ntdsutil, and then press ENTER.
metadata cleanup: connections
server connections: connect to server (DC with Domain Naming Master)
metadata cleanup: select operation target
select operation target: list domains
select operation target: select domain (%d of unwanted Domain)
select operation target: list naming contexts
select operation target: select naming context (%d of naming conext to remove)
metadata cleanup: remove selected naming context
(repeat selecting naming contexts for all specified)
After doing that, you will be able to see that references are removed from AD, and after a while, will be replicated to other servers in the AD.