I'm trying to understand your post a little bit more. "I don't have a clue where it's coming from"? Does this mean you still have a water leak? If so, it's imperative that you get that fixed first.
If the floor is damaged for 3/4 the length of the RV, then this is a pretty extensive repair. All the cabinets that limit access, flooring, etc. will have to be removed to get access to the floor. If the damage is under your reefer, heater, water heater, and such, the job gets even bigger. Once all the items are removed that limit access to the floor, then replacement is not too difficult if you have some good construction skills and tools.