Plug welding misplaced holes in structural members is common as long as the repair procedure is in conformance with AWS D1.1:2002, 5.26.5 and the procedure has been approved by the RDP.
There's quite an a lot of weld metal to be deposited in the hole which will generate a lot of heat. Unless the weld spec is specifically for this case and the weld is carried out slowly the heat could change the properties of the steel. Depends on the type of steel etc, all these details are covered by the weld spec.
I agree with Qshake. In the whole of the affected zone undertainties will have been generated that wouldn't be standing in a piece perforated anew. The deposited weld steel likely is stronger than the original, but the base steel is affected in the HAZ zone and its properties may have been downgraded in ways that make the ordinary provisions for checks under both statical forces and fatigue might not be applicable, there not being maybe standing others for the case when the steel has so been affected.
The cost of fabrication of the pieces may advice to make other kind of modification than scrapping them.
Substituting some area of plate or plates also will cause HAZ zones to be present, but you may bring the weld zones to less critical places for which the success in the repair is easier to warrant even by specifications, and so you may avoid to use the critical placements such altered holes for bolts.
