Preheat your oven to 350°F (175°C). Line an 8×8 inch square baking pan with parchment paper, leaving a slight overhang on the sides. This will help you lift the bars out easily once they have cooled.
In a medium bowl, cream together the softened butter and granulated sugar until smooth. Stir in the flour and 1/4 teaspoon of salt. The mixture will be crumbly. Press it firmly and evenly into the bottom of your prepared baking pan.
Place the crust in the oven and bake for 15 to 18 minutes, or until the edges are just starting to turn a very light golden brown. Remove the pan from the oven but keep the oven turned on.
While the crust is baking, whisk together the maple syrup, eggs, brown sugar, melted butter, and vanilla extract in a large bowl. Ensure the eggs are well incorporated and the mixture is smooth.
Stir the chopped pecans into the maple mixture. Pour the entire filling over the warm, par-baked crust, spreading the nuts out evenly with a spatula.
Return the pan to the oven. Bake for another 20 to 25 minutes. The filling should be set around the edges but still have a very slight jiggle in the center. Do not overbake, or the filling may become tough.
Remove the pan from the oven and immediately sprinkle the flaky sea salt over the top. Let the bars cool completely in the pan on a wire rack. For the cleanest slices, refrigerate the bars for at least 2 hours before cutting.