From your post, the sequence of events seems to be:
1. Action was trued.
I suppose a rifle built around this, and when shot, it printed OK?
2. Rifle was rebarreled and restocked by someone else.
Now it prints too far out for the same scope to accommodate with its adjustments?
If so, I'd send it back to the person who rebarreled and restocked it. But this has the assumption built into it that there was an original rile built on the trued action that shot fine (i.e., no excessive scope adjustment) with the same scope. If no rifle was built on the originally trued action, you still don't know.
BTW, truing an action usually doesn't include checking the "centeredness" of the scope base holes. Some may, but I'd guess many don't. And to be a stickler, it is "truing", not "blueprinting," because the steps taken in getting the thread centered usually take that thread beyond the point where a factory barrel can be used -- i.e., it is not "blueprinted" to factory specs.