When I drilled the seats for my new gibs, I tried as closely as possible to line the hole up with the seat so as to apply force only in the horizontal direction. This force would then be only met with forces normal to the base and dovetail and would help ensure a good gib contact with the rest of the base. I drilled them deep enough so that the tip of the dog screw was fully engaged.
You could try to fill it with a mig weld. It may warp though. Or maybe you could flip it over and drill new seats.