In a medium bowl, whisk together the gluten-free flour, almond flour, cocoa powder, baking powder, baking soda and salt.
In the bowl of a stand mixer fitted with a paddle attachment, or using a hand mixer, cream together the butter, coconut oil, brown sugar and granulated sugar on medium-high speed until light and fluffy, about 2-3 minutes.
Add the eggs and vanilla and mix until well-combined. Scrape down the sides and bottom of the bowl.
With the mixer running on low, slowly add the dry ingredients to the wet ingredients and mix until well-combined. Scrape down the sides and bottom of the bowl, then mix again until fully incorporated. Mix in the chocolate chips, pecans and the diced caramel squares.
Cover the bowl and refrigerate for at least 2 hours, or up to 3 days.
Preheat the oven to 350°F. Line large baking sheets with parchment paper or silicone baking mats.
Scoop the cookie dough into round balls, 2 tablespoons per ball. Place on the prepared baking sheet, about 2 inches apart.
Bake for 11-13 minutes, until the edges are set but the centers are still soft.
Remove from the oven and cool on the baking sheets for 5 minutes. Press a few more pieces of caramel and chocolate chips into the tops of the cookies. Transfer to a wire rack to cool completely.