It depends on what the adhesive used was.
If the wood is far enough gone, you can remove the bulk of what used to be wood easily enough, and then clean up the sheeting as seems best. I had good luck with a sort of solid sanding block I picked up somewhere and since forgot the brand name of, a kind of soap-bar sized brick of sand grit held together with a binder of some kind.
For the bottom of the bunk board, it would not be hard at all to put in most any sort of waterproof sheet product rather than the original Filon. A piece of countertop laminate, for instance, should work just fine.