I'm so sorry. It is heartbreaking to lose animals.
Could be all of them. Did you examine him closely for any bites? The predator might have had a nip at him and he got away. He will definitely be traumatised. I would have put the female in with him at night so that in the morning they believe they have always been together. I'd go and do it tonight. I would also get him more females. What breed is he? If he is a Campbell the recommended ratio is one drake to 7 to 10 females. Not suer about other breeds, but most of them need at elast 2 or 3 ladies.
As to protecting them there is only one sure way, since you can't logically kill all the foxes, you must prevent foxy getting in, even if it means chicken wire buried down into the ground, around the sides, and over the top, and checked regularly.
When you say the duck door was open, do you mean their run gate, or were they inside a shed? Foxes are clever but I don't think they can open shed doors or even run gates. Could anyone have let them out? Were your chickens OK? If they were, I would suspect a dog rather than a fox - one of my boys is duck obsessed and won't go near my chickens. The advantage I have is that they are gundogs and retrieve them to me so I can get them back into their run. They won't kill them intentionally.
Hope that helps