Cull the Flock, Cleanse the Earth, Start Over. Again.
I noticed three or four days ago that Blondie, our new easter egger pullet smelled funny. "Stinky chicken, but you sure are pretty," I told her. "That's okay, you'll clean up and smell just fine after you've been here a while."
Later I noticed her being a little standoffish. She and her sister, Blue would huddle in the corner together with Blondie usually stooped low. I figured it was being in a new flock. She'll get used to it here. Chickens are resilient.