I believe D1.1 allows mislocated holes go be repaired in accordance with a WPS. There are inspection requirements that must be met and the engineer has to approve the WPS to be used. There are three conditions to consider, structures that are subject to static loads only, those subject to cyclic loads, and those fabricated from quench and tempered steels. Each has specific requirements that have to be met and those requirements are more stringent for cyclic loads and Q & T steels.
My experience with the repairs of MLHs has been that if the hole is excavated so that it looks like a canoe and welded using stringers, it will pass NDT (UT or RT) will little difficulty. If the hole is simply welded using a spiral welding technique starting at the outer edge of the hole spiraling toward the center of the hole, it will be difficult to pass the NDT.
Best regards - Al