Ideas
I never let the coop get dirty either, it was the actual chickens themselves that had gotten dirty. I didn't even know that was possible at first, but apparently they can get dirty and that's when I noticed I could see them again. As soon as they cleaned themselves, they disappeared again.
Also, I saw your question to a different comment about when we started playing Cottage Living. I actually bought Cottage Living the day it was released and didn't have any issues with the chickens disappearing in their clean state back then, so I can confirm that this is not normal!
I don't play with chickens in all my households and I play rotational so unfortunately I'm not sure when exactly they went missing in their clean states, but according to my screenshots folder the rooster was at least still showing up in his clean state on 10-10-2024. Meaning it's definitely a recent bug!
Thank you so much for confirming that it's not normal. Also, thanks for letting me know that it's normal at least until 10-10-2024.
When I found this issue, even though I saw that other gameplay videos didn't have a problem, I worried a lot that only my save might be broken. So, after knowing that people currently have the same issue, I feel more relieved, but then I want this bug to be fixed someday.