Try the suggestions here: https://forums.dovetailgames.com/threads/preserved-gwe-aggregate-industries.30951/
Yep, I just tested it. Need to keep spawning the loco until you get one with a GREEN text EM2000. 2nd attempt for me, and refueling worked like a charm.
This is also listed on the road map as something they are going to fix as well, to stop the east coastway cl66 subbing in to the GWE scenario. Hopefully a fix is incoming soon so we can just run it without having to check it's the right cl66 each time.