Preheat oven to 375°F and line a baking sheet with parchment paper, and set aside. It is best to use two baking sheets and rotate them between batches. Dropping the second batch of dough on the hot cookie sheet will slightly change the structure of the cookie.
Add 2 cup chopped pecans/pecan pieces to a large skillet with ¼ cup 100% pure maple syrup, 2 tablespoons light brown sugar, and ¼ teaspoon sea salt, and cook over medium heat until the sugar and syrup have coated the nuts and aren't super sticky, about 5 minutes.
Transfer the nuts to a parchment-lined pan or plate to cool for at least 15 minutes or until ready to use.
While the pecans are toasting, whisk together the 1¾ cup all-purpose flour, 2 tablespoons malted milk powder, and ½ teaspoon baking soda in a medium bowl and set aside.
Pull the 14 tablespoons unsalted butter out of the refrigerator to sit at room temperature for 15 minutes before using.
Add 10 tablespoons of the butter to a skillet and cook over medium heat until melted. Continue cooking and stirring frequently for 2 to 3 minutes until brown bits start to form in the bottom of the pan, the top is foamy, and it has a nutty aroma. Remove from heat and stir in the remaining 4 tablespoons of butter until melted. Transfer the butter to a large heat-safe bowl or stand mixer bowl fitted with a whisk attachment.
Add the ¾ cup light brown sugar, ½ cup granulated sugar, 2 teaspoons vanilla bean paste, 1 teaspoon salt, and ½ teaspoon maple extract to the butter and mix to combine.
Add 1 large egg and an additional 1 large egg yolk and mix for 30 seconds. Let rest for 3 minutes, then whisk again for 30 seconds. Repeat the resting and whisking for 2 more rounds. The batter should be smooth, thick, and shiny when done - almost like caramel sauce.
Use a rubber spatula or paddle attachment to mix the dry ingredients into the wet ingredients for 1 minute. The dough will seem very soft, this is normal and you do not need to chill it.
Fold in most of the candied pecans, reserving about ¼ for topping.
Portion the dough out with a #20 (2.15-ounces) cookie scoop and drop the dough 3 inches apart on the prepared baking sheet. Top the dough with some of the reserved candied pecans.
Bake for 10 to 12 minutes, rotating halfway through.
Remove the cookies from the oven and use a round biscuit cutter to shape them. Allow the cookies to cool for 3 minutes on the baking sheet before transferring them to a wire rack.
Brush the hot cookies with ¼ cup vanilla simple syrup and sprinkle with Flaky sea salt.