My experience is that they'll work it out over time.
The first time I integrated chickens I thought the best result I'd ever have was 2 flocks living under one roof. And I was glad they'd gotten past the Mean Girl stuff to achieve that level of detente.
Today it's all one big peaceful family. The pullets from my most current integration still prefer their own company. One hen will occasionally send another one scurrying. But there's no blood and no clear victim or bully so my strategy is to let them be chickens.
Why do you have 2 coops? Are you OK with that arrangement?