Sorry to hear about those soft spots, I hate to say it but I'll bet it's not related to water coming from the windows or roof. Chances are it's from the wheel wells, entrance door or outdoor kitchen.
No matter, your camper will be either replaced or sent back to the factory. They have a new facility just to handle these floor replacements.
Being out of warranty you have a long uphill battle to get it done under warranty, this is where your dealer has to step up the plate.
Where exactly are the soft spots?
Ron W.