Combine all purpose flour, rye flour, fine sea salt and baking soda in bowl. Whisk to evenly distribute and set aside.
Combine browned butter, dark brown sugar, confectioners sugar and vanilla into bowl. Mix on medium high until creamed - about 2 to 3 minutes, or light and fluffy.
Add egg and mix on medium low until well combined. Scrape bowl down as needed.
Add dry ingredients to wet ingredients and mix on low. Scrape bowl down as needed.
Add chopped chocolate and pecans. Fold in using a rubber spatula until well dispersed.
Use 2 tbsp cookie scoop to scoop out dough and place on baking sheet. Firmly press dough into scoop and flatten out opening so it is flat on bottom. Place at least 2" apart.
Top with additional chopped pecans and dark chocolate.
Preheat oven to 350 F.
Bake cookies for 13 - 14 minutes, or until edges are browning and crisp. Remove from oven.
'Scoot' cookies if necessary. Top with flaky sea salt. Allow to cool before enjoying.