I'm afraid you most likely had a bear. Bears are very opportunistic, and most coop break-ins are actually because the bear is after the chicken feed. They smell it easily, and chicken feed and scratch is just FULL of the things bears love to eat to put weight on! Bears love easy meals and the feed is a lot easier than chickens. Chickens are tempting, though, once a bear is inside. They will absolutely go after chickens if there is no easier meal tempting them first.
The bear was likely after the scratch that you mentioned is gone-- they love grains, and corn, and all the better if it's easily eaten in a big pile.
The best bear deterrent is an electric fence; it's a bit of an investment, but it will keep more than just bears at bay! Bears are pretty intelligent and he or she will remember your coop area as being an easy food source. It might not return right away, but it will be back to check things out again. A bear remembers the painful surprise of an electric POP to the nose even better than it will remember the food, though!
Good luck to you! I'm sorry that you lost some of your feed.