Are your tires actually hitting the fender flares? The front is more of an issue, if you hit a bump going around a sharp corner or have blow shocks and a lot of weigh up front you can rip the fender out.
Your tire will grab the fender lip and pull it right out, not good at all. Seen it a few times. If you are lowered I would say do it, it will save you in the end.
But get it done at a decent place because if they dont do it right they will crack your paint around the edge and have to respray... Just get it done right.