RyanF,
You can plug weld the holes and re-drill, but you run the risk of making a hard spot, which can cause problems also. Others may have a better solution, I fill such holes (as well as installing a base with .495" spacing where .580" spaced holes were drilled) by plugging with a screw, "loc tited" and tightly peened in and finished off( be sure it doesn't protrude into the bolt race). If the hole won't be covered up, you can lightly countersink it, so the thread won't "run out" to a knife edge and show as a pit. Then you can re-drill and tap the hole in the correct location. Where possible, I try to save one of the original holes. Part of the new hole will be in un disturbed material, and I never had a problem with the screw "holding". I find blue "Loc Tite" is sufficient, if left to cure overnight.
Mike