Preheat oven to 350°F. Line 3 large baking sheets with parchment paper. Set aside.
In a medium bowl, whisk together flour and cocoa powder. Set aside.
To the bowl of a stand mixer fitted with the paddle attachment, add butter, sugar, salt, baking powder, and baking soda. Mix together on medium speed until light and fluffy.
Add egg and vanilla. Mix well, scraping the bowl as needed.
With the mixer on low, gradually add the flour mixture until well combined.
Using a 1-tablespoon cookie scoop, drop the dough onto the prepared baking sheets leaving about an inch between the cookies.
Using your thumb or a small teaspoon, make an indent in the middle of each dough ball.
Place 1 cherry in each indent.
To a small saucepan over medium-low heat, add the chocolate chips, sweetened condensed milk, and 2 teaspoons of reserved cherry juice. Cook, stirring constantly, until the chocolate has melted, about 2-3 minutes.
Using a piping bag or small spoon, carefully fill each cherry indentation with about 1 teaspoon of the chocolate mixture, completely covering the cherry.
Bake for 9-11 minutes or until just set. Allow to cool on the baking sheets for a few minutes before transferring to a wire rack to cool completely.