Well, this can be done, but its a big project. I recommend you take my answer as a starting point for your own research, you don't want to mess this one up. And before I start, BACKUP EVERYTHING before you do anything regarding this migration.
You didn't mention if there was any WAN connection between the two offices and if there was what kind of domain/trust structure was setup. So I'll assume there is no connectivity for sake of answering.
If you don't need to migrate existing email, your job is far easier. Assuming you do, you need to figure how to get email from Server B (the one we will retire) into Server A. There are two ways I know of. If you only have a small number of mailboxes to move the easiest is to export usersmail as .pst files and then import at Server A once their new mailbox is setup. If you have a lot to move you should look into the Mailbox Migration Tool from the BORK 4.5.
Now that the mail is moved and new mailboxes/accounts are setup you needto edit the DNS MX records to point to Server A for both internet domains. Also point your new domain that both will use to Server A via a MX record. You'll also need to edit your routing info in the IMS to accept these messages. Check this link for details:
http://www.swinc.com/resource/exch_faq_sec3.htm
Look at section 3.23 for the answer. Be sure to add the old SMTP email addresses to users info in the Exchange Admin program or the messages won't get sent to them. Now that email from both old domains and your new domain should be coming in the last thing is to give the remote site (the site that had Server B) access to their email. You have a lot of options here, some are better for convenience and others for security. You could just blow a hole in your firewall to the ports Exchange uses, but that's not a good idea. A VPN is one option, Outlook Web Access is another.
Good luck,
-Heath
