Advice needed…impermeable roofing underlayment installed incorrectly – GreenBuildingAdvisor

We are having a metal roof installed and due to not having a rainscreen or insulation on the exterior, we opted to have an impermeable membrane underlayment installed over the entirety of surface in case of condensation and to prevent moisture damage.

Our roofer installed EpiStick Pro which is a self-adhering membrane to the entirety of the roof. But, after a rainy day yesterday, we and came to find multiple places where water had leaked into the home through the membrane. Upon further inspection, we found the roofer used staples in seemingly random areas (including over some sheathing joints) all over the surface of the roof, both of which are against the manufacturer’s installation in instructions. I contacted the manufacturer and asked how to fix and they said to install another layer over the one that was incorrectly stapled. They did not even entertain the idea of patching, I’m guessing because of the sheer number of staples throughout their membrane.

Warranty compliance is our biggest concern. I am hoping for some wise advise on how best to handle this. Buying all new Underlayment will not be inexpensive for the roofer and I’m truly not sure how the roofer will respond to this news. One thing I wonder is if he will refuse but offer to cover the roof in their usual product which is a roofing felt. We hired him to install the peel and stick because we wanted something vapor impermeable. If he offers to go over it with roofing felt rather the rebuy and place a second layer of EpiStick, is this an acceptable solution? Would installing a second layer over the first that’s failed truly be a good solution versus taking it all off and redoing it?