Sorry for the lack of updates, but here is a final summary! Thank you all for the help again.
We kept the bully separated for an additional three weeks, and then did a week of daily supervised interaction in a very open, neutral, and full of distractions area, but kept them sleeping apart. There were some scuffles, but the victim was always able to escape and they resolved pretty quickly.
After that week and seeing that they were seeming to get along better, we put them back into the coop together during the day, unsupervised. This went fine, though I'm sure there were also some scuffles.
After that week, we went back to normal, and they did just fine! They are now back to being friendly and were frequently found sleeping huddled together during the winter. I would strongly recommend this re-integration plan to anyone dealing with a similar issue! It worked very well for me.