I feel your pain.
I had the same thing happen to me yesterday. I had three chickens (one Barren Rock, two Ameraucanas) and two Indian Runner ducks. I also have one Jack Russell that I am trying not to hate, that has a doggy door so he can go in and out of the house. The dog pen was closed and latched when I left for work, and the suspect was sitting on his pet bed. I even locked my chickens in their larger run, but they are accustomed to free ranging in my yard so the Ameraucanas jumped out. I came home to feathers everywhere and my dog running lose, the dog pen latched. Someone opened it, let him out, and latched it behind them!
I cant think of anything else to do but call the police and try to get a warrant for trespassing. I am certain it was one particular neighbor, or her kids. I let her son pet the chickens once when he saw me putting them into their pen. He asked if he could bring his dog over to help catch them but I remember telling him that dogs do not go well with chickens, and havent seen him show interest in them since. We even have locks on our coop so that no one but us can let them out. I have never left them in their larger run on any other occasion while I was away for more than an hour, and now I have only one lonely chicken.
I am furious with my neighbor and feel bad for my birds. The kids old enough to know what he was doing, and I am disturbed by their lack of concern for my birds lives, my property, and my dogs wellbeing (not that I care all that much for that right now). I swear my Barren Rock was making a sad sound this morning when I let her and the ducks out of the coop.
Now I have to get another chicken for her to roost with, especially since falls coming up. I can either buy another pullet, quarantine her for a while and hope that they socialize easily, or raise chicks again like I did my other girls, but I am getting married in a month and going away for a week after that so that seems like a poorly timed task. Whats the best way to replace my chicks?