Nigel: I just went through a weekend of the same kind of BS you are experiencing. I did some stereo work and did not disconnect the negative cable of my battery. I turned the car back on and had that stupid transmission fault code in addition to a plethora of other issues. I disconnected the negative cable for 20 minutes and put it back on - no more warning lights and everything worked.
I know this sounds simplistic and some experts will roll their eyes at this suggestion. Your mechanics have probably disconnected the negative cable fixing other things, but why not try it again? It will not cost you anything and its worth a shot.