I don't have a copy of API 510 handy. Does “repair” specifically refer to only weld repairs in this standard? This is important because what you are performing is a mechanical repair. If ALL repairs are implied in this standard, an API 510 certified inspector needs to review and accept your repair plan. I would follow deanc’s advice.
HOWEVER, if you don't get resolution on this matter from the API 510 inspector, other options include over sizing the holes or plug welding the existing bolt boles in accordance with the original code of construction, drill and re-tap for use.