[emphasis mine] For me, this would be enough to say "Don't Do it"!I don't see a potential problem except that when you open the breaker "feeding" a panel, you normally assume all the conductors in the panel are dead and you can start ripping into it arbitrarily. So there's potential for an "unexpectedly enlivened" safety hazard, esp. in a crowded box.
So is this prohibited? Common practice? Does it require tagging/labeling/warning/grouping or other special treatment?
I'm not exactly sure what you've got, because you seem to contradict yourself (or I'm just not taking enough time in reading).
Does the refrig. circuit go to the subpanel in the kitchen (you talk about 'nutting THHN to the Romex in the "kitchen panel")? I'm visualizing Romex running from the fridge receptacle to the subpanel and terminating on a breaker therein. Then, I'm reading that you want to eliminate this breaker (within the subpanel), and continue the Romex (via a THHN splice) to the MAIN panel. Is this correct? If so, why not just extend it with 12/2 w/ground Romex to the Main panel? You would use a separate knockout with a Romex cable clamp from the subpanel to the MAIN (at the main, you could run two cables in one clamp).
I would NOT run anything within the conduit of the feeders from the Main to the subpanel.