If I have understood you correctly... You've noticed a leak for two years and are now wondering if you take it to another dealership, will Winnebago extend your warranty for possible damage? To be honest, I have no idea.
Have you, or more exactly, is there a record of you reporting a leak? How was the problem handled? I've found documentation of problems for warranty purposes an absolute must.
If you know where the leak is on the RV, I'd be tempted to reseal the problem area myself. Maybe someone who has had a Winnebago claim will chime in.