It could be caused by over breeding, pecking or by boinking into the roof. As the male is getting his feathers back and the female isn't, my guess is that the male is pecking her and someone else was pecking the male before but that has stopped since he moved away from them. It could be over breeding (a coturnix roo should have 4-7 females) - but that seems somewhat unlikely as they shouldn't start breeding before they are 6 weeks. It also seems unlikely that boinking would cause continuous lack of feathers on the back.
I'd separate the pair until their feathers have regrown and get a few more females before reintroducing them. House the new females and the pair right beside each other for a couple of weeks before introducing them, to reduce the risk of fighting.