Sounds like everything is good for your flocks! The only other thing is that it sounds like some of the affected birds are high production hybrids. I've found that they sometimes need more protein. I had a balding red sexlink who I could NOT get to regrow feathers for over a year and a half! So...
I'm sorry about your rooster!
So you don't have any roosters in your flock anymore? It really does look like rooster damage. It doesn't look like they are molting, either. But it looks like I see pin feathers coming in in the first pic?
I'd do a really thorough check for lice and mites. DE...