Preheat oven to 350°F. Line a 9x13 inch baking pan with parchment paper, leaving overhang on sides.
In a large bowl, whisk together melted butter and sugar until combined. Add eggs one at a time, whisking well after each addition. Stir in vanilla.
Sift cocoa powder, gluten free flour, and salt into the wet ingredients. Fold until just combined, then fold in chocolate chips.
Pour half the batter into prepared pan and spread evenly. Drizzle half the caramel sauce over batter, then pour remaining batter on top. Swirl remaining caramel into the top using a toothpick.
Bake for 30-35 minutes until a toothpick inserted comes out with a few moist crumbs. Do not overbake.
Let cool completely in pan, then sprinkle with flaky sea salt. Cut into squares and serve.