In a small dish, whisk together the flaxseed and warm water. Set aside.
In the bowl of a stand mixer, combine the butter, sugars and vanilla extract. Mix with the paddle attachment on medium speed for 2 minutes.
Scrape the sides and bottom of the bowl, then add the flax mixture and mix 1 minute on medium speed.
In a small bowl, whisk together the brown rice flour, amaranth flour, tapioca starch, nutmeg, salts, and baking soda.
Add the dry ingredients into the butter mixture and mix on medium speed until the dough comes together.
Add the chocolate chunks and mix until thoroughly incorporated.
Scoop the dough onto a piece of cling wrap and form into a log about 2” wide and 12” long.
Wrap and freeze for at least 1 hour.
Heat the oven to 350F and line baking sheets with parchment.
Cut the log into ½” disks, placing them 2” apart on the sheets.
Sprinkle the tops with a bit of Kosher salt and turbinado sugar.
Bake for 11-12 minutes, until edges set and start to turn golden. They might look a bit underdone, but this is fine.
Let the cookies cool on the baking sheet for 10 minutes, then transfer to a wire rack and cool completely.
Store them in an airtight container for up to 3 days, or freeze - these make insane ice cream sandwiches!