Store the cookie cups loosely covered in the refrigerator until ready to serve.
You can make the cookie cups the day before serving; store in covered container or re-sealable plastic bag. Fill the cookie cups up to 6 hours before serving; keep refrigerated.
Preheat the oven to 350 degrees F. Grease and flour 24 mini muffin cups. Place 1 cookie dough round in each muffin cup. Gently press your thumb into each dough-filled cup, making a small indentation. Fill each cup with about ½ teaspoon chopped pecans.
Bake until light golden brown, 15 to 20 minutes. Cool in the pan, about 10 minutes. To remove from the pan, gently twist the cookie cups until they turn freely.
In a medium bowl, mix the whipped topping and maple syrup. Spoon about 1 tablespoon of the filling into each cup. Top each with pecan half.