Today I loaded the Carputing M6 program: it works!
Several parameters are now typical of a manual car: idle speed, trans oil temperature totally wrong, no tranny pressure, no commanded pressure...
Then I loaded the program back to the laptop: now it has my original VIN and the original calibration number!
At the end I loaded the A4 program (yes, I still have the automatic tranny) and everything went back to normal.

I don't know if this can be done using every program of the same year, I just know that Carputing did some modification to the program to fit my PCM.