Since GT has always been owned by CN, all you have to do is get another engine painted for CN. For a modern RR you will find GT engines nearly anywhere in the CN system.
I don't know about Proto 2000 precisely, but with other models I've had good luck using Walthers Solvaset and a rubber eraser to remove lettering - just a good pencil eraser will work. Just use lots of Solvaset and take you time and it should work OK.
Ir it possible to change the name [ grand trunk to c.n.] without ruining the paint on a proto 2000 engine? rambo1...