Melt the butter in a light-colored saucepan over medium heat, swirling often. Cook for 4 to 6 minutes, until it smells nutty and small brown bits form on the bottom. Pour into a large bowl, scraping in the brown bits, and let it cool for 15 minutes.
While the butter cools, toast the chopped pecans in a dry skillet over medium-low heat for 4 to 5 minutes, stirring often, until fragrant. Set aside to cool.
Blend the cottage cheese in a small blender or food processor until completely smooth.
Whisk the brown sweetener into the cooled brown butter, then whisk in the blended cottage cheese, egg yolk, and vanilla until smooth.
Add the almond flour, baking powder, xanthan gum, and salt, and stir until a soft dough forms. Fold in the toasted pecans and chill the dough for 30 minutes.
Preheat the oven to 350°F and line a baking sheet with parchment paper. Scoop the dough into 1 1/2 tbsp balls and flatten each one to about 1/2 inch thick.
Bake for 12 to 14 minutes, until deeply golden at the edges. Sprinkle with flaky sea salt and let cool on the baking sheet for 15 minutes before moving.