I envision two different coops that share a run. When they are in the run you had or have had some problems but when they are out with lots of room you don't have issues. They probably form two separate flocks, kind of avoid each other. They put themselves to bed in different coops. I'd guess at least a few of the younger birds have started laying. The two flocks may have combined some when the younger started laying. I could be mistaken in any or all of this.
I do something similar to what you want to do with mine, though I move the younger into the olders' coop. After they have proven to me that they can coexist in the run and free ranging I lock my youngers into the olders' coop after it is dark and the older are already in there, you'd go the other way. It's dark enough that they can't see to attack each other. I just set them on the coop floor, many people like to set them on the roost but I don't bother. They will work that out themselves and will figure out where to sleep as time passes. I'm down there at sunrise when they wake up to see how it is going every morning until I'm sure it won't be a problem. It has never been a problem but you never know for sure. Each time it can be different and your chickens and coops are different from mine.
I lock the old coop so they cannot get back in there. If your two are laying in the old coop they will have to find another place to lay. I typically do this well before they start to lay so that isn't a problem for me. Many times on the second night they put themselves to bed in the new coop. When they don't, they go to bed near the old coop. I wait until it's dark when it is easy to catch them and toss them in the new coop. If you are consistent they soon get the message.
I do not set them on the roost when I do this, just put them on the coop floor. They will determine who sleeps where based on the pecking order. I don't care who sleeps where in there as long as it is not in my nests and is predator safe. My goal when I do this is that no one gets hurt. They will work out all that other stuff in time.