I am so sorry. Was it a one story cage? Baby chinchillas can have fatal falls from ledges you may not think are very high. That is why breeders use only one story cages with no shelves or ledges. It could have also been a birth defect. Usually they will pass by their 10 day birthday if there is an internal defect, but occasionally they can last a little longer. Unfortunately, you will never know for sure what happened.
I am so sorry for your loss. I have been breeding for over 14 years and it never gets any easier when I lose a baby.