Preheat oven to 350 degrees. Once the oven is heated, spread the pecans on a rimmed baking sheet and and roast for 5-8 minutes. Watch them closely so they don't burn!
In a small mixing bowl, stir together the cacao powder, coconut flour, baking soda, and salt and set aside.
Once the pecans are done, crumble or chop 1/4 cup of them and set aside. Then transfer the remaining 2 1/2 cups to the food processor, then pulse until the mixture resembles nut butter (it will be a similar texture to natural nut butters, with tiny specs of nuts, not totally smooth). Stop and scrape down the sides of the food processor with a spatula occasionally if needed. If you have a very small processor, you may need to do this in two batches.
Whisk the sugar, maple, eggs, vanilla, and 1 cup of the pecan butter in a large mixing bowl. If you have extra pecan butter, store it in a container for another use.
Add the dry mixture of cacao powder, coconut flour, baking soda, and salt to the wet ingredients and stir to combine. Last, fold in 2/3 cup of the chocolate chips.
Line a 9x9" square baking dish with parchment paper. Transfer the batter to the pan, then sprinkle with the reserved 1/4 cup crumbled pecan halves and 1/3 cup chocolate chips.
Bake for 28-30 minutes or until a toothpick inserted in the middle is almost clean. Check them after 20 minutes or so - If the edges are browning more than you'd like, cover with foil and return to the oven to bake. Don't overbake! **Note: I use a glass baking dish - I've not used a metal pan, but I would guess it might cook more quickly.**
If you're adding the flaked sea salt, sprinkle that on as soon as the brownies come out of the oven.
Place the dish on a wire rack to cool completely (at least 20 minutes) before slicing.