The reason they are sleeping in the nest 'boxes' is because the roosts are too low and probably too small to be comfortable.The two senior ones have been sleeping in their boxes when I got them last year.
Here's a fix you might be interested in pursuing:
Here's an excellent modification to that kind of coop:
https://www.backyardchickens.com/th...ng-in-nest-boxes.1134399/page-2#post-17749535
Or you could turn that whole mini coop/run combo into a coop by removing the interior wall of the coop....since you have to 20 x 40 run area.
Pics of the 20-40 run area?