I would keep the fender bars welded on until you fill in the metal for the body work. Once that's filled in I'd cut the lower piece off the frame and back until it looks right/blends in with the body work. Having a tube like that as the fender rim is already going to strengthen the fenders. Frames flex and bodies flex when going over stuff so yes there would probably be damage of some kind if it's left solidly mounted to the frame. Sheet metal work is not the most fun and it'd be sad to see some weld crack or metal wavy after a few wheeling jaunts.