If your feral is a "he," he might have gone gallivanting. Anyway, I HOPE he's out gallivanting. We had a big feral tom that was partly tame (oh, yeah, I fed him and he'd come in the house and sleep on my lap), but he'd leave for a week or two every now and again. He always came back, except the last time, when he left the night before a BIG blizzard. We were very sad - he was a nice cat. This female we have now is one of probably four that live on our property. I know for sure there are three, and there might be another one. Don't know how many are girls and boys, but I wasn't under the impression that boy cats would kill kittens like the big cats do. I'd almost suspect mom-cat, but the dead kitten was large and perfectly healthy looking. Her belly was full, so it wasn't like mom didn't have enough milk and had to "thin the herd," so to speak. We're still quite baffled, and I hate to go on an on like this, but we love all our critters, even the wild ones, and this hurts. But maybe we'll see Streak (the mom) and her surviving baby some day. If the baby actually survived. Not like we need more cats, we have five already that live in the house with us, but it's always nice to have barn cats, especially considering the MILLIONS of mice that also live here.
The other possibility is that a weasel might have attacked the kittens while Streak was out hunting, and the Pyrs ran the weasel off before it could carry off the second baby. I'm not even sure if weasels carry off their kills, or they just eat where they kill. Ach! Listen to me. I just need to let it go.
There are at least two broody hens sitting on eggs in the barn also, and probably more out in the "hedgerows," so pretty soon there will be fuzzbutts running around and those always make me smile. I would have liked to see the kittens grow up, though.