I've repaired 3 of my 4 flares and one I've done twice! I like the look, but they are a bit of a pain.
Twice, it happened when I was backing up and caught my mud flap between my tire and a rock and it ripped the flare right off. The other time I came off a ledge and landed on the mud flap behind my right front tire and it ripped off the flare. I've since shortened up my mud flaps.
If you remove them, you have to either weld up the holes (this is the right way) or put tape on the back of the holes and use a heavy bedliner (the cheap-o way). Or do nothing, leave the holes and wheel it! (the usual way).
I don't like the look of a wide tire/wheel w/o flares, and like
@Sparky said, until something happens, don't mess with them.
Dan.