Preheat oven to 350 degrees Fahrenheit and line a 9x9 inch square baking pan with parchment paper. There will be some paper hanging out of the sides.
In a small saucepan melt your butter on low heat.
Stir in the chocolate chips just until melted and smooth. Remove immediately from heat so that the mixture does not boil.
Transfer the mixture to the bowl of stand mixture and let it cool for 10 minutes.
In separate medium bowl measure flours, potato starch, arrowroot, sugars, cocoa powder, xanthan, and salt and whisk together. For best results use a scale. Set aside.
Once the ten minutes of cooling have passed, in a small separate bowl activate your egg replacer with water (at cool temperature to avoid clumping). Let sit one minute to thicken.
Next add the activated egg replacer and vanilla to the melted butter and chocolate. Mix on low for 1-2 minutes or just until combined.
Remove the mixing bowl from stand mixer.
Fold in the dry mix with a spatula just until combined.
Pour batter into the middle of lined baking pan and spread it out evenly with spatula. Batter will be thick.
Bake for 35-36 minutes.
Let brownies cool completely.
Serve and enjoy!