Preheat oven to 350°F and line two baking sheets with parchment paper.

Whisk together flour, cocoa, baking powder, and salt in a medium bowl. Place chopped chocolate and butter in a double boiler or in a heat-proof bowl over a saucepan of gently simmering water. Slowly melt the chocolate, stirring occasionally until smooth. Remove from the heat and set aside to cool slightly.

Combine eggs, sugars, and vanilla in a large mixer bowl fitted with a whisk attachment and whisk together on medium speed for 5 minutes, until pale and doubled in volume. Reduce speed to low and beat in melted chocolate for 1 minute. Add flour mixture and mix on low speed for 20 seconds, just until combined. Fold in chocolate chips.

Use a medium cookie scoop coated lightly with nonstick spray to form the cookies and space them 2 inches apart on the baking sheets (bake 10 cookies per baking sheet).

Bake cookies for 12 to 14 minutes, rotating pans halfway through, until tops are shiny and crackly. Remove from oven and sprinkle with flaky salt. Let cookies cool for 10 minutes on baking sheets, then transfer to a wire rack to cool completely.

Brownie cookies are the most fudgy and tender when freshly baked. Store leftover cookies in an airtight container at room temperature for 1-2 days. You can also freeze any leftover cookies for up to 2 weeks.