Claus,
You should call PowerChips about this, as they know this area well.
My understanding is that the ECU does relearn your new driving style and parameters, so I assume it is reset with the new program.
Have you considered giving PowerChips a shot to create a program for your mods? I know you haven't been happy with the Hamann/Superchips setup, so maybe it's time to try something new. I think you will be very happy with the results!
FYI, they have the ability to dyno tune the car as well... Although their core business is selling ECU programs which are mostly adaptive on their own, they are tuning my friend's twin Garrett ball-bearing turbo 996TT and they will be the core of my tuning program for my M5.
BTW, have you lost any bottom end torque from your cams? I am planning to do Hamann or Evosport headers, and was wondering if it is worth it to do cams.
Also, is it worth going through the trouble to fit race cats? How much power are they good for?