In a medium mixing bowl, combine gluten-free flour blend, baking soda, salt and rground cinnamon. Whisk to combine. Set aside.
In a large mixing bowl, add melted butter, brown sugar, and granulated sugar.
Cream with an electric mixer for 2-3 minutes, until light and fluffy, scraping down the sides of the bowl with a spatula as needed.
Add the eggs and vanilla extract and mix until smooth.
Add half of the flour mixture to the butter mixture and stir until just combined. Repeat with the remaining flour, stirring until no more streaks of flour remain.
Stir in 1 ½ cups of the chocolate chunks and 3/4 cups of the toasted pecans, reserving the rest for later.
Chill the dough for at least one hour.
Preheat the oven to 350°F (175°C). Line a baking sheet with parchment paper.
Scoop the dough into 2-3 tablespoon balls. You should get about 24 dough balls in total.
Place the cookie dough balls on the prepared baking sheet, leaving at least 3-4 inches in between each one. I can typically get 6-8 cookies on a sheet at a time. Place any remaining dough balls in the refrigerator until ready to bake.
Top the cookie dough balls with the remaining chocolate chips and toasted pecans before baking. This will help you get chocolate pockets on top of the cookies as they bake.
Bake in the middle rack of the oven at 350°F (175°C) for 10-12 minutes, until the edges of the cookie are lightly browned and the middle is no longer shiny. Let cool on the baking sheet for 4-5 minutes before removing to a cooling rack to cool completely. Sprinkle the cookies with flaky sea salt right after removing them from the oven. Repeat with remaining dough.
Once the cookies have cooled, enjoy!