The best "first thought" answer I can give would be to ask your AI. 

From an opinion point of view, if the vessels is new then I would see no reason for "R" stamping if the vessel can be reworked by the original manufacturer WITH THE CONCURRENCE OF THE AI!.  In this case, it would be reworked, re-hydro tested and a new data report would be issued and signed.  I can almost gurantee that the AI will not go for heating and bending a part to correct a dimentional descrepancy..this could be argued that unecessary stress could be introduced into the vessel.  I you built the vessel, contact your AI.  If it was built by another mfg, send it back and have them correct it, but make sure they do it correctly (AI involvement).

Now, regarding technicalities of the NBIC - Nowhere could I find any mention of the scenario you described requiring a "repair".  Seems to apply to "welding".  However, under appendix 6-3000, examples of alteration, "d" says that "a change in the dimensions or contour of a pressure rtaining item" is an ALTERATION.

Hope this helps.