@Lilion : it's supposedly not supposed to happen, but my first hatch of chicks was also attacked by my rooster Théo. He attacked the broody Chipie as well as long as she kept the chicks, and she defended them fiercely, even though she was much smaller. I think he saw the chicks as strangers who had stolen his girl. They were not his chicks, so maybe he knew it. She was also like yours, being bullied by the rest of the flock, and I think her low status also played a part.
It was frightening enough that I let them live completely separated from him during the day; they were in the same coop at night, though. Real trouble for the chicks began when they were weaned at six weeks, and the rooster quickly took the broody back as "his" hen. She was no longer protecting them. But at six weeks they were sufficiently independent and clever to handle it.
I don't think a time out for your roo Mannie will necessarily change his behaviour, but it will allow the chicks to grow, be less fragile, and when you put him back the rooster will probably be at first more busy with the hens than thinking of the chicks.
On the other hand, I tried separating my rooster for just a few hours daily. I did it both with Théo last year, and again with my other rooster this year to protect his tiny hen Piou-piou who was wounded. They hate it absolutely. I couldn't do that to a rooster for days. It just makes them utterly depressed.
I’m not really legitimate to give advice, as i’m just beginning to see a way out of my rooster drama

. But I agree with
@rural mouse. Roosters mate, especially in the morning and evening, it's their main point in life. Why should they hide from you? You're not a dominant rooster. The only thing different I would add, is that for some of my older hens, coming to peck my leg is a way to protect themselves from being mated. So while I let the roosters mate in front of me, I don't let them do it close to the point of almost touching me, that feels like stepping on my foot.
There’s a lot of conflicting advice on how to handle roosters. But if something doesn't seem to make sense to you, you should take it with a grain of salt

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@notabitail i’m sorry for your loss. You posted lots of beautiful pics of chicken Abigail here. I can't say I feel like I knew her, but I know she was very special to you among your chickens. If or when you feel like it you could post again some of those pics of her.
I feel like you that those moments when you count the chickens are one of the most painful after a loss. It takes time.