If your rifle was tapped at the factory, then they will most likely take your rifle apart and put it back together with a new receiver. Same old barrel stock etc.
Depending on how far off the holes are, a gunsmith could either mill them out to 8-40 or if the holes are off too far, he'll ask you if you want new holes that will require the rail to also be re-drilled for the new holes.
I heard of people using epoxy under rails but I would not go that route personally.
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