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Very good point...I failed to say in my post that my pen or crate is in the barn so they can all see each other...If you do think separation is warranted, because Momma is small and timid, I would try to create an enclosure where she is still in visual contact with the rest of the flock. For example, if you have the space for it, sectioning off part of the coop with hardware cloth, so she is still "with" the flock, but she and her chicks are safe. That will make it easier when her chicks and older and everyone gets put back with the main flock. If you remove her entirely, the flock may see her and chicks as strangers when they return, and it will be rough on them.

