So... I think the best idea (combining all of our ideas) is:
Put a "pop door" in the side of the barn, extending from that pop door is a run which is covered in chicken wire/ netting. Then, for the chores, you can nail netting to the inside of the door creating a huge flap curtain of netting...
Oh NO! :( What a horrible thing to be experiencing.. here are some things I can think of... may be useful, may be not.
A sonic low pitched pest deterrent? I have seen them on Ebay, may deter the owl? May disturb your chickens though...
Netting of some sort seems to be the only real option...