Preheat oven to 375 °F (191 °C). Line baking sheets with parchment paper or silicone baking mats.
In a medium bowl, whisk together flour, baking powder, salt, and baking soda. Set aside.
In the bowl of a stand mixer fitted with the paddle attachment, cream together butter, light brown sugar, granulated sugar, and powdered sugar until light and fluffy, about 5 minutes.
Add the egg yolks, egg, and vanilla extract and mix until incorporated. Carefully add the flour mixture to the bowl and mix until dough forms.
Using a spatula, fold in the chocolate chunks.
Using a large cookie scoop, scoop dough onto prepared cookie sheets and sprinkle sea salt flakes on top.
Bake 10-12 minutes (the cookies will firm up as they cool if they still look soft to you).
Let cool for 10 minutes on the cookie sheet then transfer to a wire cooling rack to cool completely.