It's always best to slope any flat areas AWAY from the walls or house.
A simple wedge-shaped "shim" cut from a 2x4 to give you the proper slope will act as a new "rafter" before you re-sheet with plywood.
Nothing wrong with going over the existing membrane to build your sloped roof, but better to remove membrane to make sure you don't have rot or other unseen issues.
4x4 posts should NEVER be toe-nailed into a membrane deck, only asking for problems. You could incorporate a base pad mounted to the deck, and then flash with membrane. This gets the contact point up off of the deck. Some have mounted the 4x4 right to the deck, then flashed with membrane up the 4x4 itself to a height of 3 or 4".
The best option, if it works for your application, is to re-build your railing system so that it mounts on the OUTSIDE of the perimeter of the deck area, so that nothing penetrates the membrane roof.
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