I am going to get the software updated on mine. So what I am going to do is put the old controller back in so everything gets updated and once home install the new controller.
Or the other way is to specify at the start of the update that a new hardware had been installed. I don't know how the update would react to this given that the new controller is not recognised by the computer specific to the car.
The best bet is to remove the controller and put th old one in for the time it takes to update and swap straight after. Simple.
Lugnut, with yours if you put the old controller and update it will simply update the component it failed to update the first time. This can be done while you wait. 10 minutes max. Good luck!
E92 M3 2007 - ///PE with Test Pipes and BPM Stage II; CF Interior & Splitters; CIC with Connected Drive