1997 MGF VVC :
If I swap out the Engine management ECU for a replacement the garage says it won't work due to mismatch with the alarm system?
Your garage is correct. The alarm transmits a code (called an EMS code) to the engine ECU. If the ECU receives a different EMS code to the one it expects, the engine will not run. In this way the engine ECU and the alarm are "matched".
The good news is that pscan can "rematch" ECUs. So, you can buy a used engine ECU and install it into the car, and then use pscan to "relearn" the EMS code and then the replacement ECU will now be happy with the alarm.
There is a video showing the process here
The video shows "relearning" the EMS code from a Simtek emulator, but the principle and process is the same.