I did the same thing over and over when I had the factory flairs. Here what I did. I don't have carpet, so if you do pull it away from the wall right behind the passenger seat. There will be an ovalish hole on the tub filled with foam. Start pulling the foam out and you will see the other side of the clips. Get some long ass needle nose pliers and pinch the clip and they will pop out. Attach them to the flair and push them back onto the body.
2013 Billet Rubicon
Ace rock rails, 2.5 teraflex coil lift, AEV Geo brackets, Rancho 9000xl shocks all around, 35x12.5x15 Wrangler MTR's on Mb chaos wheels, Bushwacker flat flares, 12k winch on Rough Country hybrid bumper, Spyder rear bumper/carrier, KC long range windshield lights, rock lights and some other happy crap.