Preheat the oven to 350°F (175°C). Line two baking sheets with parchment paper or silicone mats.

Make the Cookie Dough:
In a large bowl, beat the softened butter, granulated sugar, and brown sugar together until creamy. Add in the eggs and vanilla extract, and continue mixing until fully combined.

In a separate bowl, whisk together all-purpose flour, cocoa powder, baking soda, and salt. Gradually add the dry ingredients to the wet ingredients, mixing just until combined.

Stir in the melted semi-sweet chocolate and mix until smooth and well combined. The dough will be thick.

Chill the Dough:
Place the dough in the refrigerator and chill for at least 30 minutes to help the cookies hold their shape while baking.

Prepare the Coconut-Pecan Filling:
While the dough chills, prepare the coconut-pecan filling. In a medium saucepan, combine shredded coconut, chopped pecans, evaporated milk, egg yolks, and sugar. Cook over medium heat, stirring constantly until the mixture thickens and turns golden, about 5-7 minutes. Stir in the vanilla extract and remove from heat.

Shape the Cookies:
Once chilled, use a cookie scoop or tablespoon to form 1-inch dough balls. Place them on the prepared baking sheets, spacing them about 2 inches apart.

Bake the Cookies:
Bake in the preheated oven for 10-12 minutes, until the edges are set but the centers are still soft. Let the cookies cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely.

Add the Coconut-Pecan Topping:
Spoon a generous amount of the coconut-pecan filling onto the center of each warm cookie. Allow the cookies to cool completely before serving.