So once when I was playing Pokemon X, I decided to shiny hunt. I was using the chain fishing method and hooked a shiny Luvdisc. So I used my level 100 Farfetched and got the shiny to 1 hp, but then it used Take Down. So it died. And I was screaming inside.
Make sure to check if a shiny learns a move that hurts the user, like Explode or Take Down. If it does at that level, use a Quick ball and then Ultra Balls or Timer Balls.