Well, we have a new possibility. So we currently have 2 chickens inside with GI issues. One is resolving, but she shit has some diarrhea, the other one is slow emptying and she has zero desire to eat so we've started liquid tube feeding her.
However, yesterday, as we were bringing that second one to the vet, our flock boss started acting weird. I noticed she was shaking her head and had her wings kind of low. She went to go lay and I thought maybe that's all it was, but then the egg she laid was a softshell! So we brought her with us to the vet. He suspected mycoplasma! She's done the head shaking thing on and off in the last year and a half, and I have seen maybe 3 other soft shell eggs in the past but never caught who was doing it. So we sent a sample to be tested. The vet said that mycoplasma *could* explain the GI issues on the other two girls, even though they aren't having respiratory symptoms. It would also explain why the emergency vets that have been taking care of the two GI cases never tested/suspected mycoplasma.
Anyway, it'll be a week or so before we find out. Meantime, we have 3 chickens in the house and the one with the respiratory symptoms is VERY depressed being alone in a crate inside away from her flock. She's never had any other health issues to bring her inside so she's definitely not okay with this arrangement

Worried we are stressing her out, but don't want the other birds to get sick, even though they've probably already been exposed.