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That is an excellent question.

You would have to realign the neck using whatever technique you are comfortable using in that situation. I'd floss it which isn't any fun with the fretboard on but I can make it work. If it was really off you'd have to re-glue the fretboard I guess. How would you approach that problem?

I've got a jig that keys in the truss rod slot and allows me to drill locating holes in both the neck and fretboard and use 1/8" wooden dowels as pins. I mark the centerline of the fretboard and dry clamp everything and bolt on the neck to insure that the fretboard is indeed in the centerline. I usually glue the dowels into the neck with everything clamped up in perfect alignment so one site of possible movement is eliminated.

Even with snug locating pins I have seen little shifts during glue-up so I really watch the centerline marks on the fretboard relative to the truss rod slot during clamping.

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