CAN synchronisation and protocol diagnostics

I have a 2013 Navara that I’m looking at doing an engine swap on. The big end has spun and therefore I can’t run the engine. Does the engine need to be running to do some CAN protocol diagnostics? My main concern is being able to have the auto transmission operate correctly with a different ECU(Haltech elite 2500) and engine(VK56de). I know that with the ECU you can have two separate CAN systems, 1 for the Haltech gear and sensors and 1 other but I’m not sure about whether the factory CAN system will integrate properly. Would the HPA CAN course answer these questions? (Haven’t yet enrolled as I’m still unsure of whether I’ll be able to do the swap)