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Ahhh yeah that will do it unfortunately... 
You can also remove chickens from your farm if you run into something like that again.
If you go to the chook menu, click an individual chook, you can use the garbage can icon to remove said chook from your farm.

Be careful with those gold chooks though!

Just logged on today.... I had 75 chooks before. I now have 9 chooks, and i was going to delete them all and start again but none will delete, and it keeps saying *blank* has left your farm for some reason... Oh, and my happiness is at -119. I guess that means I'll have to restart...

Do you mean that when you loaded you only have 9 left, or did they all leave after you loaded?

We're looking into it, but this is the first we've seen of this bug. They cant leave unless you are active on your farm, the only thing we can currently think has happened is some sort of corruption or editing of the main save file.
Again, massive apologies you've had this experience, and Im happy to sort you out with a boosted save if you contact me directly via contact@trilumstudios or join our disc and hit us up there.

Both really. About a quarter of the ones that left had left when i was offline I think