Your pony, your choice!
I have a beautiful Night Glider and a visible part of her body is discoloured; as she was a grail pony that I wanted to keep and display, I decided to use a few thin coats of carefully-mixed acrylic to touch-up the blemish. Unless you look very closely, you cannot see the blemish! There is also scope to remove this thin layer of paint in the future, should I choose to.
If you intend to sell the pony, I am sure potential buyers would like to know up-front. Some collectors don't mind, yet others feel it super important to have an untouched, original pony, so here is where the issue lies!!