I would guess that she did have failure to thrive. Probably some metabolic disorder that you would never have known about or a thyroid disorder.
Telling your kids has got to be the worst. How old is he? My daughter has been away at camp this week and two of our goats kidded, we lost one of our babies. I was really not looking forward to telling her about the baby we lost, but she was able to focus on the babie she was going to meet when she gets home tomorrow. She's 13.
I hope that you're son is able to grieve over his lost friend and recover. Maybe he'll ask for a new friend when he is ready, and by then you'll be ready too?
I'll say a prayer that the right words come to you.