When the car is updated the computer will use the latest available software. So there is no worry as to which version will be installed.
It's very important to return the car to original factory spec before updating any software. Once the update s done then plug-in the updated/latest hardware.
These computers are like Windows 95 and will not recognise new hardware unless specified at the vehicle identity stage as per my post in another thread.
I am getting my car updated on Friday, and when I take it in, I will plug-in the old controller so that the programming will go without a hitch. Hopefully.
E92 M3 2007 - ///PE with Test Pipes and BPM Stage II; CF Interior & Splitters; CIC with Connected Drive