No, the situation has not been resolved. The problem with alllowing the contractor to spot repair, is he first said there was no metal on the front face of the house(the one in the pictures), after looking in the attic he changed to they don't where they put all the metal. Yes, I realize the could spot repair the front and other sides but what about the rest of the metal. At the end of the job from what I could see left of the flashing and fascia, about 65 ft of 2 foot aluminum flashing and 140 ft of aluminum fascia went on the roof. The lumps in the roof don't seem to account for it all and he didn't seem to want to deal with the ski slope affect along the eaves(caused by improper nailing of the drip edge ?). The question is do you now have a new roof or a roof thats been repaired in so many spots, that it's going to be a ongoing headache.
I searched the internet and could not find any reference to metal being used to repair a roof deck as standard practice. Most said replace wood with similar wood. A few said maybe for knot holes or a hole from plumbing stacks. As you pointed out metal does not grip nails.
The roofing consultant is a good idea, I will keep it in mind if I have to take this further. The last I heard from BP was a e-mail that included copies of their warranty and installation instructions. I guess they don't want get involved.
You are correct about the BP shingle installation instructions. Even more interesting are the application intructions for the BP grip guard. "Remove all shingle,felts,nails and metal from roof deck area"."Always apply gripgard directly to wood deck".
As for the estimator, I have had several people out that one can only imagine why a professional in his field would do a complete 180 basically destroying his own creditability.