Multiecuscan

I have been having EGR/MAF issues with my Stilo JTD and want to perform an ECU reset. I am, however on my second engine.

At some point during the engine swap over I believe that the ECU had to be reprogrammed to accept a new injector. If I perform an ECU reset, am I in danger of resetting to an earlier sstatus and screwing up the injectors?

Clearing fault codes won't affect mapping or injector coding, as they are stored in different memory.
Clearing fault codes will just reset the memory that holds fault codes and learned sensor behaviour such as fuel trims etc. Anything that has been specifically coded to the car will not be reset.