This is similar to swapping the idrive control in an early '08 car to the newer version. When you go to update the software it will fail if it finds the new controller. For this whenever I take the car for an update I put back the old idrive controller for a complete integration.
The BMW software update system is smart and will pick up even the smallest annomoly. Also when updating the software on the BMW system you cannot carry out the update for individual components. You have to do the who car.
The other issue with the software update is that components may fail during the integration especially the telephone control module. The dealers won't take the responsibility for the component failure and so does BMW. Hence the reason they don't offer free update or encourage updates unless there is an obvious issue with car. If one is prepared to replace the failed component and prepared to pay for the workshop time for a total integration - which could be as long as 6-8 hours - then stealer will perform the update for you.
I have been though all this in the first two years of ownership. Thank you very much.