Sounds like my luck.
I just installed a set of Schumacher shortys so I put studs in. One head had one stud in it so I left it alone but I knew it was going to be trouble. After putting in the other 11 studs and torqueing them, I went to put the nut on that pre-existing one and it just sort of fell out. I put a longer stud in it and it threaded in way past the shoulder and I couldn't torque it. Now I'm afraid to torque the nut because it doesn't seem to be getting tighter although the stud isn't turning. I figure I'm down to the last good thread in that hole and don't want to pull that one out too.
i would just helicoil and move on.
While I understand the concern of using using bolts in place of studs. I've bee doing do for 50 years without issue. I normally use a high temp sealer (copper or red). Using a wooden Q-tip I put a small amount in the threaded hole and on the end of the bolt, install and "elbow torque". Can't say I remember ever having an issue and if I did, drain the coolant, repeat the above on the offending bolt. Much easier than drilling out a broken stud in the car IMO
Most headers I've seen over the years do not give enough clearance to use a regular sized nut and require the bolts with undersize heads
