Preheat oven to 350°F. Line a 9x9 inch baking pan with parchment paper, leaving overhang on two sides.
Sift together flour, cocoa powder, baking powder, salt, and baking soda in a medium bowl. Set aside.
In a large bowl, whisk melted butter, brown sugar, melted baking chocolate, eggs, egg yolk, and vanilla until smooth and glossy.
Gradually fold dry ingredients into wet mixture using a rubber spatula until just combined. Do not overmix.
Gently fold in three-quarters of the cherries and chocolate chips. Reserve some for topping.
Pour batter into prepared pan and spread evenly. Scatter remaining cherries and chocolate chips on top.
Bake for 35-40 minutes until edges are set but center has slight jiggle. Toothpick should come out with moist crumbs.
Cool completely in pan before lifting out using parchment overhang. Cut into 16 squares.