Some things i noticed: I tried duplicating the bugged model, and the wireframe box extended far beyond what should've been the actual model.
I was also using the Advanced Bonemerge addon, and when I unmerged the smaller models attached to the bugged model, they didn't appear above the bugged model, where they'd normally appear.

did you move feet/hands too far away? could be that you messed up their physmesh, and how were you resetting their position? with stand pose tool? as ragmover's resets only work for nonphysical stuff

I went back to the save this happened in, and it appears to have fixed itself???
I honestly have no clue what happened, but I'll try to describe what was going on then.

1. From what I could tell, the arms and legs weren't initially that far, they just suddenly decided to be 10 miles away from the model. I was however dragging around the center if the gizmo, which seems to behave strangely sometimes, so maybe I did it accidentally.
2. When I was resetting their position, I did it by right-clicking Reset All or Reset +Children All on the bugged bones of the physical model. Nothing happened, so that may explain it.

Hopefully this helps.

and you say you did also try to reset the gizmo offset? and what was thw issue with moving it by the center of the gizmo, you weren't holding down shift when moving with it?

Oh, I actually didn't notice the center of the gizmo changed behavior when holding shift.
And yes, at the time I tried resetting the offset as well.
The issue hasn't happened since either, maybe it was a one time occurrence or user error.
Sorry for the inconvenience.