Yes. It will conflict with your remap and it may not even be possible to remap the new software. Basically the fix involves reducing NOx without any effect on power, torque, fuel economy or CO2. But reducing NOx means increasing soot, which has to be burned off in the DPF and requires additional fuel. To do this without affecting power, torque, fuel economy or CO2 the software changes the injection pattern, so fuel is now pre-injected, followed by a main injection, followed by a second main injection. Obviously, for this to work, the injectors have to be in tip top condition and the EGR valve stem must not be worn. Problems have arisen when injectors were old, dirty or worn and where the EGR valve stem was worn.