It is very heartbreaking
I lost 7 to a fox because I wasn't watching them closely while they were free ranging. I learned though you can't prevent every possible thing that may happen but it's best to learn from it.
I would just double secure everything and frequently check your coop and run for any signs of predator attempts. I check my coop and run a couple times a week top to bottom just to make sure nothing has been trying. I would try to get a trap because whatever it ended up being, will most certainly be back.