Last year the homeowner had hired a :flat roof specialist" to install 2 skylights. The contractors idea of installation was cutting out the roof openings, placing the new $800 skylights in, and caulking them. This manner of installation does not work in any way at all.
Once we removed the 4 layers of roofing, we noticed large water stains coming down the walls. This was a tell tale sign that the roof leaks were caused by more than just a failed roofing system. We presented the problem to the owner, as well as a solution, and installed a new rubber roof.
To fix the siding issues and prevent further roof leaks we removed all siding. We installed a new vapor barrier, new insulation board, and re-flashed all windows. We then installed a gutter on the higher roof to keep water from cascading onto the lower and bouncing off of the wall. This new flat roof and siding system should last 20 years with proper roof maintenance.