The no risk, high dollar approach is to rip off everything, inspect and replace damaged decking, then go back with whatever roofing system you choose. This option is favored by many roof consultants and roofers as they are guaranteed there is no moisture remaining in the roofing or damage to the deck. Under certain conditions this is the proper approach. Under other conditions this is wasteful of the owner’s resources and un-friendly to the environment. Removing the roofing to the deck incurs larger costs for the labor and disposal of the old roofing material as well as the usual installation of thicker insulation to meet your state’s building code.