I originally did the standard cut and fold about 8 years ago. They were just spit welded shut by a buddy. Collected water dirt and mud. Didn't really notice until I was expanding my wheel wells, and they were all nasty and rusting out. I cut all but about a 1/2" to 1" lip on either side and welded in some 18g fully welded by a buddy, seam sealed, and painted inside and out with primer then undercoating.
If I were to do it again, I'd just trim all but a lip and weld in new steel, seal and paint as everyone above mentioned