Decks, Patios, Porches and Docks - Slate Patio Install Need Help

I am installing a slate patio on a 4th floor. The patio was torn out and replaced because of water leaks. The roofers laid decking, then a flashing pan and then tar mopped it to complete the waterproofing process. Now that we are ready to lay the slate we noticed a little movement from the flashing pan. My question is when we lay the slate should we lay concrete thick enough to make the metal flashing lay flat then a layer of thin set? We have an installer, but we want to make sure he is going to do this correctly, we spent a lot of money waterproofing and he has already suggested that we put screws in our waterproofing. Which is not happening, so we are trying to find other ways to make this flashing lay flat.