Any wet roofing materials need to be removed and if those wet materials are next to the deck then the deck needs to be inspected for damage and repaired, overlaid with new decking or replaced. With that stated the issue is whether just the wet materials be replaced or does the entire system(s) need to be removed. While there are some other considerations that will require the complete roof removal (addressed later), it really boils to down cost. Figure out which type of new roofing system you want to use then obtain a price to install this new roofing system as a “go over” by replacing all wet areas with insulation of a thickness that matches the height of the surrounding area with a new system installed on top of the old. Then obtain a price to remove the entire roofing system(s) and install a new roof system. If the difference between the “go over” and complete replacement to you is substantial, just replace the wet areas and install the new roofing system over the old. If the difference to you is not substantial – go with the complete removal of the existing system(s).