They are living animals with their own wills, their logic doesn’t always work like we think it will. In other words they will do what they want. We can usually strongly influence them though. I know we’ve discussed some of this before on other threads but I can’t remember details of what your old coop looks like or how many ISA Browns you have. I certainly don’t know what the new coop looks like.
I’ve found the best way to get them to lay where I want them lay to start with is to use fake eggs. Does that always work? No, it doesn’t always work, but it helps me. You can get all kinds of different opinions on what the nests need to look like, how open or dark they need to be, what size, where they are placed, or what bedding to use. People are successful with a wide range of nests but sometimes they just lay wherever they wish anyway.
I built a couple of my nests so I can lock a chicken in there if I wish. When I catch a hen laying where I don’t want her to lay I lock her in a nest until she lays an egg. That works practically all the time but it’s not that easy to catch her on her other nest, especially if you are gone during the day. That’s the only thing that I’ve found to work for me.
I know you said you want nests that you can empty from the outside instead of having to go through the coop to get to them. The more restrictions you put on things the more challenging it can be to achieve everything. You may have to do some compromising or work harder. Which do you want more, eggs you can get from outside or poop free eggs?
Normally a chicken’s instincts tell them the highest place they can get to is the best place to sleep, but chickens can be trained to sleep somewhere else. Some instincts aren’t that strong in some chickens. Also some chickens are just brutes on the roost. They terrorize other chickens that try to sleep close to them. Most chickens like company when they sleep but some don’t. That may be why some of your ISA Browns slept in the nests, the others were beating them up on the roosts so they looked for a safer place to sleep.
So what can you do to get them to sleep on the roosts instead of your nests in the new coop? First put the roosts in noticeably higher than the nests. If you don’t do this you don’t have much of a chance. Don’t shoehorn them into the tiniest space possible. Don’t think of magic numbers of how many inches they need on the roost per chicken, give them plenty of room to spread out. Give the ones sleeping in the nests a chance to get away from the bully without going to your nests. I’d suggest putting in a separate roost, higher than the nests but lower than the main roosts and separated a few feet so they have a safe haven if they need to get away from a bully. Will this always work? No but it will greatly improve your chances of success.
Do your ISA Browns have a way to get to the roosts? They should be able to easily fly up five feet or more to get to a roost as long as you haven’t clipped wings. But they need enough room to spread their wings and fly or maybe a series of steps they can jump up, but they also need room to get down. Restricting their room can have bad effects on their behaviors and limit their options.
If you can do this, they may still not sleep where you want them to. If that happens you need to place them where you want them to sleep after they have gone to bed. This means you have to have access so you can pick them up and put them where you want them to sleep. That can be challenging in some coops. You also need it to be really dark, otherwise they’ll just hop down and go where they want to. If you have lights outside of windows that can be a challenge. Since they are laying and you won’t be down there to open the nests really early blocking off the nests to force them to sleep somewhere else isn’t a good option either. I’m not criticizing you for that, I’m not down there that early myself, though when I’m integrating I do try to not wait too long to get down there.
I don’t know what stage your new coop build is in. I don’t know how much flexibility you have in it, the smaller it is the less flexibility you have. My main suggestion after putting in high roosts with a way they can get to them is to just try it. See what happens when they get new digs. You may not have a problem, you may. If you have a problem you can’t live with, you can try to fix it, but sometimes that isn’t easy.
I think your main problem could easily be that you have a hen that is a brute on the roosts. That would be consistent with my experiences. You may have just had really bad luck on the personality of one hen. If you can determine which one that is, remove her from the equation for a few days and see what happens. Isolate her and see how the others react without her. Your easiest solution could be to use the subtraction part of chicken math.
Good luck!