Your floor is probably not rotting, but simply poor construction.
If it is like the new Flagstaffs, the floor is made up of a sandwich of two very thin pieces of plywood, and I use the term loosely, with the floor framing and styrofoam in between. The three layers are glued and then squeezed together until dry. This makes a very light, but very pathetic, floor.
The "plywood" they use is actually just luan, the same cheap crap they use under the fibreglass skin of the outside walls. It is very poor quality, an much weaker than regular plywood. FR uses it because it is cheap.
Unfortunately, over time, the thin plywood will flex as you walk over it, and the styrofoam underneath will begin to crush. That just gets worse and worse, resulting in a 'soft' floor. It is worse if you have heavy-footing people, or kids, stomping around in the camper. We don't even wear shoes in ours!
The only solution I can think of is to skim the low spots with the kind of mud they use to finish under vinyl flooring for your house, then lay down some laminate flooring, with the planks going across the floor joists. You should have enough space under the slide to lay down 3/8 laminate, and the slide can always be adjusted a bit if not.