Unfortunate: upon being told to kill a shiny, your pokemon will not turn to your trainer and provide a dialogue box saying "Excuse me, [player name], but it appears you have commanded me to attack a shiny pokemon. Would you like to undo this action? Yes/No"
It's been confirmed that Pokémon in auto-battles won't differentiate shiny Pokémon. They will still try to defeat them without a warning to you.
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