Feathers Falling Off On Back Of Neck?

How old is the one pictured? Could it be molting? IF you suspect it might be your rooster causing it, then the easiest solution is to separate him for awhile, until the feathers have grown back in. It will be easier to reintroduce him back into the flock, than to remove a hen, reintroduce her, and have to re-establish pecking order. Yes, you will get more roosters when you hatch, so prepare in advance as to what you are going to do. My bachelor pad consists of multiple, individual smaller coop/run areas, that are fine for one rooster. I have them separated with 1/2 x 1/2 inch hardware cloth, so they can't do any real pecking, or spur damage to their neighboring rooster.
 
Re bachelor pads and choice of mates. I have two surplus males in a bachelor pad. They crow a lot and breed each other but they don't fight per se. Both have some ruffled feathers on their backs from breeding. You can keep males together, they won't try to harm each other but they will take turns breeding each other. Use hides (see below) so they can take a break from each other when they want.

Re roo preferring one hen over another, this is common. I have four hens with one roo and he prefers the biggest, fattest one, who is also a paler colour than the others. Her back and neck feathers are ruffled and she has a bald patch on the back of her head. This is normal. The male grabs the hen's neck or back feathers to breed, but if she's not in the mood she will struggle and twist out of his grip, causing her to lose feathers. Game birds will naturally drop feathers when alarmed, this is a defense against predators that allows them to escape a predator's grasp.

So it's normal, and harmless, for a hen to lose feathers or get twisted/ruffled feathers from the male breeding her. What is NOT normal is all feathers from the neck and/or back being stripped off (bare skin) or any wounds or blood, especially on the back of the head. If this happens you need to remove the male immediately, or set up a partition in the cage so they're separated but can still see each other. I have had to do this with a pair of my button quail. He nearly killed her by nonstop pecking at the back of her head until she was badly wounded. He also tore all of her feathers from her back, from head to tail. They are growing back now. I believe he started attacking her because she had stopped laying eggs.

To prevent overbreeding you need to give the hens places to hide. Do not use boxes where they can be cornered. Hides must be open ended. Lean pieces of wood or tile against the sides of the cage, use plants in the corners (real or fake) or get curls of cork bark they can hide behind or under. Cork bark is lighter than wood and waterproof for cleaning. You can get cork bark at pet stores that sell reptile supplies. Any live plants should be non-toxic because the quail may try to eat them.
 

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