On my previous '93 Prowler 19ft TT, I re-positioned its axles under its leaf springs by folllowing http://www.rverscorner.com/articles/axles1.html
For my TT, it raised its chassis approx 4.5" - which created more ground height for its rear plumbing. The negative side, I had to get a large plastic box for another step. But overall, great mod. And yes, I'd do it again - on that specific trailer.
The guy who owns a 5er across the street re-positioned its axles as well. Today's pickups are higher off the ground. And, his older 5er was too close to his pickup box. He's happy to re-position his trailer leaf springs as well.
I cannot see how re-positioning axles (under leaf spring packs) would void factory warranty. But... Best to ask your Jayco Dealer to confirm....