The two engines in the Maine wilderness have been repainted. In fact whoever did so used a yellow primer so as the black paint begins to peel off they are looking very sad.
So I can think of:
1) Baldwin #60,000 at the Franklin Institute
2) At least one of the EBT engines
3) Possibly one of the Pennsylvania RR collection locomotives
4) A forgotten Heisler in a shed
5) C&O Allegheny at Henry Ford Museum
6) A sugar plantation Porter with traces of paint left
7) Sierra #34 which qualifies as it was repainted by the Sierra RR while still in service even though it was no longer owned by them.
Anymore?
Display engines somewhere that have never been repainted?