If you don't plan on using the 2nd set of holes again just get yourself some fuel resistant epoxy and glue them up.....
That would be sufficient to plug the holes. But you should sand them clean and add chamfers.
If you want to make it perfect, sand down about 0.1"/2.5mm, patch with epoxy and fibre, sand flat and paint with topcoat. Sand again with fine grid and polish. Nobody will notice the repair afterwards.