Part of the feather loss is probably molt. But not roosting and laying in bedding can cause irritation and feather loss as well. It also increases the risks of things like breast blisters, which is like bumblefoot but on the breast. Yucky to have to treat.
Do they have roosts available? If they are all molting and not laying, I would close off nest boxes and go out every night and put them on the roosts after dark. If they are still laying, then just put them on the roost/s after dark. If it's dark they are more likely to stay there. Try to get them in the habit. It may take some time as I'm sure they are very set in their ways. But unless there is a reason they are not able to roost, then that would be healthier for them.