TROUBLE with Filon roof

I would rebond the roof back to the substructure. There are a number of good adhesives to use but in the case of what you are describing I would use something with a high viscosity like a polyurethane adhesive so it flows into the disbonded area.If you already have epoxy resin I would use that thinned with a solvent like acetone. If not the polyurethane will be cheaper. I would drill a .250 to .375 hole through the skin then inject the adhesive using a hypodermic needle and a piece of plastic tubing. If you drill the hole in the middle of the disbonded area you can see and feel the structure underneath to insure it is still good as you believed. After you inject the adhesive roll from the hole to the edges of the disbonded area to ensure adhesive get to all the area that was disbonded. After curing just seat the hole with caulk or if you use epoxy just use it for a seal. This would be similar to a sidewall delamination repair. If the disbonded areas are in the middle of your roof and not around any cutouts in the roof as I think your are describing in your op it is probably not due to water intrusion but rather to the adhesive failing.