You are correct in thinking SP2 has a section of the service pack that checks for valid licensing of the software. I have seen what you are running into, on a prior job.
Prior to installing SP2, it goes out and checks for any violations of the End User License Agreement and will render the OS practically useless if EULA is violated. It is some sort of Microsoft validation tool that the name slips my mind at current time. I guess my memory is not what it use to be, huh?
Once the validation tool is run, there is no turning back. However, if you call microsoft, instead of registering MS products over the internet, when registering the software, they can help you move that license to a new machine. You are not violating EULA by transfering the license to another machine as long as that other machine goes off line.
Prior to registering your software, promote it into the domain, replicate with it, then demote the other DC. You will have up to 21 days to do so, and then the two SBS machines will conflict. Then, CALL microsoft and register the license over the phone. Explain the circumstances with them by telling them you are moving that valid license to a new machine.
There are a lot of extra steps when moving licenses around.
