Lillion:
I guess I'll try to catch her tonight when she's sleeping and move her back to the main coop. But I am a bit concerned. I've not had chickens long enough to know what to do when the pecking order changes so dramatically.
I agree 100% with
@ManueB . The only thing I would add is to see if you can put more 'obstacles' and visual barriers in the run - give her someplace to run to/hide from, Tres. Something low enough she can duck under, but Tres can't get on top of her (something with 1' of height or so - not much more - like an old coffee table or something similar), and hang old grain bags, opened up scrap pillow cases, etc. strategically so the hens can get behind them and be 'visually hidden'.
FYI: I once got an old woden coffee table for free, placed an opened up grain bag over it so the 'long sides' of the coffee table were covered, I then put 2x2's the length of the coffee table (either side) - this held the bag in place - but also created a bit of height over the top of the coffee table - and then I screwed 2 roost to that. It gave them an elevated place to roost/hop onto, AND a hiding place for the hens (actually, I've had Roos running through that, too, to get away from a more dominant rooster when they tried to poach their hen!!!
The only other modification I did was to screw the legs onto 2X4s running the length to try to keep the legs from rotting. I've had it ?9? years - wow has it really been that long I've had chickens now?? Well, anyways, I've once had to trim the legs a couple of inches due to rot, and replace the 2X4 runners under it - and it is still going strong - and the chooks still make good use of it.