Nailing deck through secondary water barrier?

I recently had a new roof installed in South Florida with Owens Corning Weatherlock peel and stick water barrier and Duration shingles. After I had a wind mitigation inspection we discovered the deck was not renailed with #8 ring shank nails every 6" per code. The roofer admitted they may not have renailed the entire roof and want to tear off some of the shingles and nail through the secondary water barrier and then replace the shingles.

My question, is it advisable to nail the deck through the secondary water barrier? Is it even possible to remove the peel and stick without damaging the deck. What are your opinions on fixing this so it meets code and passes wind mitigation.

Thanks for reading