Heat the oven to 350°F and line a baking sheet with parchment. Whisk the almond flour, cocoa powder, coconut flour, baking soda, and sea salt together.
Beat the softened butter and allulose until creamy. Beat in the egg and vanilla, then stir in the dry ingredients.
Scoop 12 dough balls onto the pan and flatten them to about 1/2 inch thick. Bake for 10 to 12 minutes, until the edges are set, then cool completely.
Melt the butter for the topping in a saucepan over medium-low heat. Whisk in the heavy cream, brown monk fruit sweetener, and egg yolk, then cook for 3 to 4 minutes until thickened.
Stir the shredded coconut, pecans, and vanilla into the warm caramel mixture. Cool for 10 minutes so the topping becomes spreadable.
Spoon the coconut pecan topping onto the cooled chocolate cookies. Let them stand for 15 minutes before serving so the topping settles into a thick, chewy layer.