Prep the Oven and Pecans: Preheat your oven to 350°F. In a food processor, combine 1 cup of the whole pecans and the brown sugar. Pulse until the mixture resembles a coarse meal.
Make the Filling Base: In a large bowl, whisk together the maple syrup, corn syrup, cinnamon, vanilla extract, flaxseed meal, milk, oil, and sea salt until smooth.
Combine Ingredients: Add the pecan-brown sugar meal and the chopped pecans to the liquid mixture. Stir until everything is well combined.
Add Flour: Gradually stir in the flour, 1 tablespoon at a time, until the batter is thick but still pourable.
Assemble and Bake: Pour the batter into the unbaked pie crust. Arrange the remaining 1 ½ cups of whole pecans on top in a decorative pattern.
Bake and Cool: Bake for 45 minutes, or until the filling is set and the crust is golden brown. Let the pie cool completely on a wire rack before slicing and serving. This allows the filling to firm up properly.