Further research suggests that if the shavings in the bottom of the coop are deep enough, you won't have a smell problem, and you can pull them all out in spring to compost them over summer. I don't think he'll be sold on the idea though. I'm trying really hard not to name the two prettier hens... But Henrietta, Olga, Ernestine, Frances, Pearl, Agnes, Ruth, Winifred, and even Omeletta have come to mind. But for right now, I just call them "beautiful" - "Hey beautiful, what are you up to?" Except the naked neck. Her name is definitely Turducken.
I did have to cull the one sick kit in Penelope's litter today, but otherwise, most of the bunnies are now symptom-free, or symptoms are improving. If the healthy bunnies remain symptom free, they will be available again 10/30. If the quarantine section isn't 100% healthy by then, they will be culled and their cages and that whole corner of the barn will be sanitized. They will be available after they have been symptom free for at least 30 days (11/29 at the latest). It seems like the comfrey is helping. The one sick kit in Penelope's litter had something else wrong with it. Her head would vibrate every time we petted her. Seems like whatever caused the neurological deficit may have also contributed to a poorer immune system. It's the only bunny in the barn who hasn't improved with the addition of the comfrey.