I ran into this issue yesterday and ended up cutting a hole in the bed and re-welding the nut to the frame. I plan to bed line my truck afterwards so I figured i didn’t have much to lose.
I’m not entirely sure, but it looks like the reinforcement plate under the bed at each fastening place might be the mount for said fastener. I’m going to attempt to remove one where I had another bolt I had to cut the head off and see if I can repair the nut. I plan to rivet the plate back on afterward.