I guess I'm the odd man out here...
I use a fresh #11 Xacto knife and scratch stuff off. It can usually be done well if done very carefully.
Here is a stock Atlas GP39-2.
To patch this for CSX, I scratched off the road number under the dynamic brake section (pretty easy).
And I scratched off the yellow shield from the cab and the battery box (a bit harder).
And this is the end result.
This is not a re-painted model.
It is stock with the unwanted ink-printing scratched off and new decals added.
(with a little bit of chalk weathering).