In a small saucepan, combine the dark brown sugar, heavy cream, egg, vanilla extract, and corn syrup. Stir in the chopped pecans.
Place over medium heat and stir constantly until the mixture begins to bubble and thickens slightly (about 5-8 minutes). Remove from heat and let the filling cool completely.
In a large bowl, beat the softened butter, granulated sugar, and light brown sugar until pale and smooth. Add the egg yolk and milk and mix until combined. In a separate bowl, whisk together the all-purpose flour, baking soda, baking powder, and salt.
Gradually add the dry ingredients to the butter mixture, stirring until a smooth dough forms. Cover the dough and chill in the refrigerator for at least 30 minutes.
Scoop 12 equal portions of the chilled dough and roll each into a ball. Place the dough balls onto baking sheets lined with parchment paper, spacing them about 2 inches apart.
Gently press your thumb or the back of a small spoon into the center of each ball to create a well. Spoon about 1 teaspoon of the cooled pecan pie filling into each well. Reserve any extra filling for topping after baking, if desired.
Preheat your oven to 375°F. Bake the cookies for 8-10 minutes, until the edges are lightly golden and the filling starts to bubble.
Remove the cookies from the oven and let them cool on the baking sheet for about 5 minutes before transferring them to a wire rack to cool completely. If you like, you can top each cookie with a little extra filling or a few extra chopped pecans.