Heat oven to 350 degrees F. Line 2 large baking sheets with parchment paper.
In a medium bowl, whisk together the flour, cocoa, baking powder and salt; set aside.
In the bowl of a stand mixer with the flat beater attached, cream the butter and sugar at medium speed until light and fluffy, about 3 minutes. Scrape down the sides of the bowl with a rubber spatula as needed. Add the egg, vanilla and cherry flavoring; beat at medium speed until combined, about 30 seconds. Add the dry ingredients and beat at low speed until just combined, about 30 seconds, scraping down the bowl as needed.
Place the ½ cup sugar for rolling in a shallow bowl. Roll a heaping tablespoon of dough into a 1½-inch ball between palms, roll the ball in the sugar, and then place it on the prepared baking sheet. Repeat with the remaining dough, spacing the balls about 2 inches apart. Using your thumb, make indentation in center of each ball. Fill each indentation with a cherry.
In a small pan over low heat, combine chocolate chips and condensed milk, heat until chocolate is melted. Spoon 1 teaspoon chocolate mixture over each cherry, spreading to cover cherry. Bake 10 to 12 minutes. Cool the cookies on the baking sheets about 3 minutes; using a wide metal spatula, transfer the cookies to a wire rack and cool to room temperature. Store in an airtight container at room temperature.