In a large mixing bowl, whisk together flour, cocoa powder, baking powder, and sea salt until well combined. In a separate bowl, cream butter, light brown sugar, and granulated sugar using a hand mixer until fluffy and light in color, about 2-3 minutes.

Add egg yolks and vanilla extract to the creamed butter mixture, blending until smooth and uniform.

Gradually add dry ingredients to the wet ingredients, stirring gently until just combined.

Portion out the dough to create 32 equal balls, each about 1 inch in diameter. Place them on a baking sheet lined with parchment paper. Make an indent in the center of each ball using a measuring spoon. Chill the shaped cookies in the refrigerator for at least 1 hour.

Preheat oven to 350°F (175°C) and bake the cookies for 9-11 minutes. Gently re-press the indents after baking, then cool on a wire rack.

In a small saucepan, heat heavy cream until simmering. Pour over chopped chocolate and stir until melted and smooth. Mix in cherry preserves.

Fill the center of each thumbprint with ganache, then chill in the refrigerator for 10-15 minutes to set.