I've had owls take 2 of my female ducks. They came out to hunt early when the sky was overcast. Now I put my babies in their pen a little earlier in the day as well as out later in the mornings.
How old is he and could it be his mating ritual. I'm a new duck mom and thought my male was choking, sounding almost like a donkey then realized it's part of his mating. Anyway hope your duck is alright.