Preheat the oven to 350 degrees and line an 8-inch square baking dish with parchment paper, leaving an overhang on the sides. Grease the sides of the dish.
In a microwave-safe mixing bowl, melt the dark chocolate and butter together in the microwave on high for 1-2 minutes, stirring every 30 seconds until smooth. Set aside to cool slightly.
In a separate bowl, beat the eggs, granulated sugar, vanilla extract, and salt together vigorously using a standing mixer or handheld whisk for at least 3 minutes until light and fluffy.
Pour the melted chocolate mixture into the egg and sugar mixture, and stir until well combined.
In a small saucepan, melt the butter for the pecan pie filling over medium heat. Add the maple syrup, brown sugar, heavy cream, vanilla extract, and salt. Stir until the mixture is smooth and slightly thickened.
Remove the saucepan from heat and stir in the chopped pecans. Set aside.
Gradually add the dry ingredients (gluten-free flour) to the brownie batter and stir until there are no flour pockets left.
Spoon half of the batter into the prepared baking dish. Spread the pecan pie filling evenly over the batter. Top with the remaining batter, spreading it to cover the filling.
Bake in the preheated oven for 25-30 minutes, or until a toothpick inserted into the center comes out with a few moist crumbs. Avoid overbaking to maintain a gooey texture.
Remove from the oven and let the Pecan Pie Brownies cool completely in the baking dish on a wire rack.
Once cooled, use the parchment paper overhang to lift the brownies out of the pan. Cut into squares and serve.