Branch offices are typically a very lean setup, 1 may be 2 servers. The number of users at the location can range anywhere from 5 to 70.
If its a single server setup, it poses additional challenges when trying to consolidate the domains. Active directory domain migration tool cannot migrate domain controllers. Demoting the only controller means the file server will lose all the ACLs.
The only solution is to move out the DC role to another box. The problem is that you may have to clean out one desktop machine and install Windows 2003 and promote to domain controller.
There is another way. Install VMserver on the desktop OS, usually Windows XP or Vista. Install a guest OS for Windows 2003. Join domain and promote as a domain controller. Move all the roles over. Demote the actual server.
Use the ADMT wizard to move the file server to the consolidated domain. Thereafter you can decide on how to handle the user accounts. Or promote the file server back as a domain controller using “Additional DC” option. Transfer back the FSMO roles from the virtual to the file server.