Make the maple pecan praline first. In a small saucepan, combine the chopped pecans, maple syrup, brown sugar, butter, and pinch of salt over medium heat. Cook, stirring frequently, for 4 to 5 minutes until the mixture is bubbly, thick, and deeply caramelized.
Pour the praline mixture onto a parchment-lined plate and spread it thin. Let it cool completely, then break or chop it into small pieces. Place the pieces in the freezer for 30 minutes.
In a medium bowl, whisk together the almond flour, tapioca starch, baking soda, cinnamon, and salt. Set aside.
In a large bowl, beat the softened butter and brown sugar together until fluffy, about 3 minutes. Add the maple syrup, egg, and vanilla extract and beat until smooth. Gradually add the dry ingredients and stir until a dough forms. Cover and refrigerate for 1 hour.
Scoop about 2 tablespoons of dough and flatten it in your palm. Place 2 to 3 pieces of frozen praline in the center. Wrap the dough around the praline, sealing it completely and rolling into a ball. Repeat with the remaining dough and praline.
Preheat your oven to 350F (175C) and line two baking sheets with parchment paper. Place the stuffed cookie balls 3 inches apart on the prepared sheets.
Bake for 12 to 14 minutes until the edges are golden and set but the centers still look slightly soft. Immediately sprinkle each cookie with flaky sea salt.
Let the cookies cool on the baking sheets for 10 minutes. When you break one open, the center will have pockets of gooey, caramelized maple pecan praline that taste like a warm pecan pie wrapped in a soft, buttery maple cookie.