Line a small plate or baking sheet with parchment paper. Scoop 14 level teaspoons of nutella, roll quickly into small balls, place on the parchment, and freeze for at least 1 hour until solid.
In a medium bowl, whisk together gluten free all-purpose flour blend, cocoa powder, baking soda, and salt. Set aside.
In a large bowl, beat softened butter, brown sugar, and granulated sugar with an electric mixer until light and fluffy, about 3 minutes. Beat in the eggs one at a time, then add vanilla extract.
Add the flour mixture to the wet ingredients and mix on low speed until just combined. Fold in the chocolate chips with a spatula. Cover the dough and refrigerate for 30 minutes.
Preheat your oven to 350 degrees F and line two baking sheets with parchment paper. Scoop about 2 tablespoons of dough, flatten it slightly in your palm, and press a frozen nutella ball into the center. Wrap the cookie dough completely around the nutella ball and seal it, then place seam-side down on the baking sheet. Repeat with remaining dough and nutella balls, spacing cookies 3 inches apart.
Bake for 11 to 13 minutes until the edges are set but the centers still look soft. Immediately sprinkle a pinch of flaky sea salt over each cookie.
Let the cookies cool on the baking sheet for 10 minutes before transferring to a wire rack. Serve slightly warm for the best gooey nutella center.