Place an oven rack in the center of the oven. Preheat the oven to 300 degrees Fahrenheit. Line 2 baking sheets with parchment paper or silicone mats. Set aside.
In a small bowl, combine the chocolate and butter. Place the bowl over a pan of barely simmering water and stir occasionally until the chocolate has melted and the mixture is smooth.
In the bowl of a food processor, finely chop the chocolate covered espresso beans. In a medium bowl, whisk together the chopped espresso beans, hazelnut flour, all-purpose gluten free flour, cocoa powder, baking powder and sea salt.
In another medium bowl, whisk together the sugar, flax eggs, water, and vanilla extract. Gradually add the dry ingredients and stir until thick and smooth. Fold in the melted chocolate. Stir in the chocolate chips. If the mixture is too dry, add 1 tablespoon of milk at a time until mixture becomes wet. Depending on the brand of flour you use, you may need more than one tablespoon of milk.
Using a cookie or ice cream scoop, scoop level ¼ cupful of the batter onto the prepared baking sheets. Bake until slightly puffed and the tops begin to crack, 18 to 20 minutes. Allow the cookies to cool completely on the baking sheets and serve.
Always read the label to make sure all ingredients are gluten free. If you are not sure the product is safe, check with the manufacturer.