Hi Sean. The engine ecu, is matched to the immo ecu. Thus if you renew the engine ecu, then a brand new one is in 'new born' mode, thus will accept the first immo code sent to it when the ignition is switched on. If the wire from the immo to the ecu is cut (pin 13 I think) then the engine ecu will not lock into immo mode & will work o.k. without it.
T4 (or AD100) can rematch the engine ecu to the immo.
Most ecu remanufacturers can reset the eng ecu to new born, thus you can choose to cut the immo connection, or allow it to match to the immo.