This is fishy in many ways:
1) Yes, to replace with an AGM, you do need to reprogram and register (I just did this on my 535). It's a straightforward process.
2) The SAT radio does not need to be touched by the programming process.
3) A new version of the car software does not need to be uploaded to the car to reprogram the battery.
4) BavAuto is not a BMW dealer (it's an independent shop), and would not have access to connect to BMW to reflash the car (perhaps they're suggesting taking it to the dealer, Weatherford, for them to reflash?)
I live in Marin. Let me know if you want help with reprogramming. I have the cable and the needed ECS software.