Pour 2 tablespoons pecans into a small bowl; set aside. Stir remaining pecans, flour, and margarine together in a bowl; press pecan mixture into the bottom of a 9x13-inch baking dish.
Bake in the preheated oven until crust is golden, 15 to 20 minutes. Cool completely.
Beat confectioners' sugar, 1 cup whipped topping, and cream cheese together in a bowl until smooth; spread mixture over cooled crust.
Beat milk and pudding mix together in a bowl until thick and stiff; spread pudding over cream cheese mixture. Stir remaining whipped topping and reserved pecans together in a bowl; spread over pudding layer. Sprinkle chocolate chips over the top. Refrigerate until chilled, at least 2 hours.