Went through all this nonsense last July. The first time I painted my flares, I did it "in situ" and hated the result. No matter how hard you try, one or more of the flares is installed so tightly that you are just not going to get any masking material behind them, resulting in some overspray. Some guys don't mind, others (we anal-retentive, detail-oriented, control freaks) are driven coo-coo by overspray.
Bit of history here...those blind fasteners are called "rivnuts" for rivet-nut. Some of you guys know them by the term "nutsert" but they are actually an old WWII airplane fastener that got ordered and used over time by another war materiel supplier - JEEP. There is a difference. Incidentally, I've never seen a rivnut on an airplane or Jeep that was any count. They're junk whose only value is to get fairings or other lightly stressed components installed in a hurry in the production environment.
The problem the TJ flares have, partiularly on the front ones, is that there's so little room to wield a cutoff wheel inside the flare because the "backside" of the wheel runs so closely to the flare itself. Forget unthreading the fastener (bolt, capscrew, whatever you like to call it) so you're going to have to cut or grind the bolt head off. Having done that the flare slips right off - easy, huh?
What I finally discovered was a Dremel cutoff wheel, about 3/4" in diameter running right down through the bolt head as though you were going to turn it into a straight-slot screw. Now here comes the nasty part...once you've cut the first slot, rotate the hex head about 90 degrees and cut another slot. Then rotate again and cut the third one. Now, with just that much metal missing, you can use a cobalt burr to grind the head down to the stem. Those little capscrews are so hard that to just try grinidng would result in two or three ruined burrs by the time you got all the way around the Jeep.
Once you've got the flare off, then you can carefully grind the rivnut and fastener stem so you're almost down to the fender. At that pont, you can easily knock the rivnut into the body with a 4 oz ballpeen and a drift punch.
Then, when you're ready to put it all back together, you can ream the holes to fit nutserts and assemble everything with new hardware.