Line 3 cookie sheets with parchment paper and set aside.
In a medium bowl, whisk together flour, salt, baking powder, and baking soda. Set aside.
In a stand mixer fitted with the paddle attachment over medium speed, beat butter, sugar, and cocoa powder until well combined, about 2 minutes, scraping down the bowl as needed. Add eggs one at a time, mixing well after each addition Add the cooled, melted chocolate and mix until just blended. Stir in the vanilla extract.
Add the flour all at once and mix on low speed until just blended. Scrap the sides of the bowl to incorporate the dough and cover with plastic wrap. Place the dough in the refrigerator for about an hour.
Preheat your oven to 350° Fahrenheit.
Once your dough has chilled, using # 70 cookie scoop or a rounded teaspoon, drop spoonful of cookie dough about 2 inches apart on your cookie sheets.
Bake until the cookies are puffed and the tops are cracked, about 10-11 minutes.
Remove your cookies from the oven – And as soon as your cookies are out, use the rounded side of a ½ teaspoon measure to make a small, deep well in the center of each cookie. Let the cookies sit on the cookie sheet for a few minutes – and then transfer them to a rack to cool completely.
Assembly: Spoon or pipe melted dulce de leche into the wells of the cooled cookies and sprinkle with sea salt. Set aside until the dulce de leche develops a film on the surface.
These cookies can be stored in an airtight container (separated by a piece of parchment for up to 3-4 days.
Makes about 50 cookies.