Preheat the oven to 350°F. Lightly grease a 9 x 13-inch metal baking pan and line it with parchment paper, leaving an overhang on two sides.
Spread the pecans on a baking sheet. Toast for 6 to 8 minutes, stirring once, until fragrant. Let them cool and then chop them into large pieces.
Place 1 cup of butter in a light-colored saucepan over medium heat. Cook, stirring frequently, until the butter foams and the milk solids turn golden brown. Immediately transfer the butter and browned bits to a large heat-safe bowl. Cool for 10 minutes.
Whisk the granulated sugar, brown sugar, cocoa powder, and espresso powder into the browned butter.
Add the eggs one at a time, whisking well after each addition. Whisk in the vanilla.
Fold in the flour and salt just until combined. Fold in the chocolate chips.
Spread the batter evenly in the prepared pan. Bake for 17 to 20 minutes, until the top is set around the edges but the center remains underbaked.
While the brownies bake, whisk together the melted butter, brown sugar, corn syrup, maple syrup, eggs, vanilla, flour, salt, and cinnamon.
Stir the toasted pecans into the filling.
Slowly spoon the pecan mixture over the warm brownie layer, working from the edges toward the center. Spread the pecans evenly.
Return the pan to the oven and bake for 27 to 34 minutes. The edges should be set, and the center should have a slight wobble without appearing liquid.
Place the pan on a wire rack and cool completely for at least two hours.
For cleaner cuts, refrigerate the cooled brownies for 30 to 60 minutes.
Lift the brownies from the pan using the parchment paper. Sprinkle with flaky sea salt and cut into 16 squares.