I am so very very sorry you have to go through this.
I don't think your other chin killed him. There would be some signs, even subtle ones that a fight was the cause.Though she could have flicked him a you'd have found him in a clump at the bottom of the cage.
Most of us here whom breed have found one like that, and have never know for sure.
If he was fine that morning,I would be inclined to think injury.They can sure ricochet around the cages. A fall or a head injury could cause severe enough injury.
They can also choke on something they've chew off some place they shouldn't have been able too.
And yes it's quite possible there was something wrong with him from birth.
You could have a necropsy done to know for sure. Just in case it's something that could be passed to your other chinchilla.
Do keep an eye on her for the next little while.