I am still waiting for a description of the set up, what type of fencing, is the coop closed at night, does the run have a cover over the top???? Pictures would help us with this also. .
What ever it was racoon, possum, skunk, owl, weasel, rat, whatever...something is wrong with the coop or run.
The coop i have today is a direct result of different preditors showing me where the weakness were in my coop and run.
everyone here has had losses and will be a great resource for you if you will show us what you have, and once you do we can maybe help you not to have any more horrible losses like you just suffered.
you will always have preditors.
You can not rehome them all.
More just move in to take their place.
good luck! And again, sorry about your ducks.