What about fabricating some kind of shim that tapers to nothing at the edges but is about half an inch high, or slightly crowned in the middle? Glue it down well in the affected area and then use the great suggestion above for the Eternabond.
The shim could be a rigid but flexible nylon type plastic, water proof and will not come apart. Glue to the roof so there is no fastener penetration.
A piece of 1/2" thick acrylic may work. It can be shaved down with an electric hand planer. I know this can be done because I have done it with some of the sunrooms I build. I have a little Makita electric planer that is set for a very shallow cut. Multiple passes will contour the acrylic the way you need.