I think you should have your Eagle inspected by someone - probably a professional - that has the knowledge to determine what caused the floor to change conditions. You know you don't trust your dealer, so you can eliminate that step. As far as the cost goes, you have to decide what it's worth to you. Material and labor can add-up quickly. That's why it's important you work with someone that knows what they are doing. If you're handy, and decide to tackle the job yourself, you will get a lot of good help on this forum. Most of us have some ideas of what might have happened to your floor, but can't go much further without being there. Pictures and good narrative are helpful.
I doubt if Jayco is willing to warrant a condition on an '08. ... don't know what your extended warranty covers - I would check with them first.