Do I just eventually let them fight it out?

Ok this will take some monkeying around, and sound crazy, but has worked well. Move the flocks, put flock 2 where you have flock 1, and vice versa. Do this at night when they are easy to catch.

Chickens are very territorial, they KNOW their territory and will defend it, but they also know when they are not in their territory, and act timid, and bring on the attack. In the new place, they gain some territorial rights, and birds see the 'strange birds' in their territory and get used to it. Leave them 2-3 days, then take down the barriers.

While you are waiting, add a lot of clutter to both sides of the run. A LOT of clutter. Pallets up against the wall, up on cement blocks, pieces of cardboard making mini walls, roosts, ladders, sawhorses. All of this will make the run seem like a strange place to the chickens, and give a lot of hideouts, and escape places. It should be a bit difficult for an adult person to walk through, but not impossible. Chickens really like things that they can get under or on top of. It will look cluttered, but actually gives more usable space as the vertical space is usable.

THEN take down the separation and let them all out. Wait one more day and night and then close up the small coop.

Mrs K

ps - or you can get pin less peepers.
 

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