strip and re-paint
I had the same problem with a similar vintage engine mount and canopy frame, not yet installed. I removed all of the powder coat with paint stripper and cleaned back to bare metal followed by steel primer and then 2-pack polyurethane top coat.
If you are talking about an engine mount that is in a flying plane I don't know of an effective way of spot repairing, because it will probably continue to flake off and rust due to the poor quality of the Vans early powder coating and prep.