An interesting question. Apologies for being 5 months late.
I'm not sure I can tell you where to allocate your scrap quantities, that's really up to how you want to track that value internally. If you want my opinion on the topic, I would allocate it to the shotpeen operation.
Now for rework. I don't know your customer or your specification. If you have MRB authority, you can attempt to rework the part to dimensional limits as long as you stay within the tolerance limits of material removal allowed by the drawing or the specification, if they exist. Other options include mechanical bending, though not generally permitted (or advised) to perform plastic deformation. I have seen situations where parts are stress relieved using a thermal treatment and re-shotpeened and the results are more favorable. All of these options really depend on the product requirements so do a thorough review of those.
Moving forward, if its an entire lot that is warped, I recommend looking at how you machine it to reduce machine stresses and look at changing your peening sequence to peen different areas first. Other options would be to reduce the intensity, reduce the coverage, or machine the part to a "before shotpeen" tolerance so that it is in tolerance after shotpeen. This will require serious rigidity in your shotpeen process so that results remain consistent.
If none if this is what you wanted, please ask the question again with more information.