Hi -
Are both domains in your merged organization in the same Active Directory forest? Same Exchange server or different ones? Are you using unified messaging (same inbox for voice and email messages) or just voicemail only? It would also be good to know what version of Unity you are using, version of Exchange, and what version of Exchange Unity is currently partnered with. Unity has specific requirements for integration with AD and Exchange, that is why I am asking so many questions. Here is another forum train that discusses this and may be of help - https://supportforums.cisco.com/thread/308842?tstart=0&viewcondensed
Regards, Ginger