Preheat your oven to 350 degrees F (176 C) and line an 8x8-inch metal baking pan with parchment paper. Set aside.
To a large mixing bowl, add the coconut sugar, gluten-free flour blend, almond flour, cocoa powder, flaxseed meal, and sea salt. Whisk to combine until almost all of the flour and cocoa powder is incorporated. Next, stir in the chocolate chips.
To the dry ingredients, add the boiling water, melted vegan butter, and vanilla extract. Use a spatula to fully combine, stirring for 30 seconds to 1 minute. The chocolate chips will mostly melt at this point, so if you would like extra whole ones for pops of chocolate, fold them in after the mixture cools a bit.
Transfer the batter into the prepared baking pan and bake for 35-40 minutes — until the edges look set and the center looks barely shiny.
Let the brownies cool in their pan for AT LEAST 30 minutes before slicing and digging in. The brownies will be super gooey before cooling and will be very hard to cut. If you would like your brownies to have perfectly crisp edges, refrigerate them for 2 hours before cutting. Store the brownies lightly covered at room temperature for up to 2-3 days or up to 1 month in the freezer.