If possible:
Tap the holes.
Plug them with a shouldered plug that leaves less than 1/8 to a 1/16 of the shoulder above the top surface, use some locktite if possible to prevent the possiblity of it backing out in operation.
Peane the plug to fill and flow over the top thread.
Then machine the surface flush.
Odds are you will not ever be able to find the plugs if you do it correctly. I used to be a master at repairing booboos when I was a machinist it is an artform, I have never received a customer complaint on a reworked part.