Ah, those little pieces of $h!t. They are called rivet nuts, or rivnuts, or nutserts, or threaded inserts. I replaced all of them on my roof with new ones. I can't sugar coat it - it was a major pain in the ass. I just used the crush/riveting method that they are designed for (along with some silicone to seal the holes), but the BEST way to install new ones is to tack weld them to the inside of the roof. This will likely cause slight damage to the paint on the exterior of the roof (that would probably be covered by the rack anyway). Either method requires dropping the entire headliner.
See my post about mid-way down this page for details on how I replaced them, along with some helpful photos:
https://www.sccxterra.com/smf/index.php?topic=1527.1680Here's another post I made a while back where folks were recommending the tack-weld method. Not as much info here, but gives you an idea of my journey with these:
https://www.sccxterra.com/smf/index.php?topic=3010.0Final piece of advice: use a thread sealer when you install the bolts again, whether you're re-installing the OEM rack or an aftermarket rack. The OEM bolts have a small rubber washer on them that is supposed to help seal the threads, but they're usually pretty torn up the first time the bolts come out. Water can seep through the threads and into the truck, even if the new rivnuts are sealed tightly against the roof. Thread sealer is basically like loctite that doesn't harden... a couple of drops on the threads, and it'll keep water from getting in. I picked up a tube of it for like $4 at Auto Zone, and I think it was actually loctite brand.