Preheat oven to 350. Line 2 baking sheets with parchment paper.
If using flax eggs, combine 2 tablespoons ground flax seeds with 6 tablespoons warm water. Mix well and set aside. (Skip this step if using eggs.)
In a medium bowl combine flours, quinoa flakes, flaxseed, baking soda, sea salt and ground cinnamon.
Beat together the butter, applesauce, and sugars on medium high speed until fluffy, about 3 or 4 minutes. Add eggs, one at a time, ensuring the first is fully incorporated before adding the next. Add vanilla and reduce the speed to low. Add in flour and beat until just combined. Stir in chocolate chips.
Drop in spoonfuls onto prepared baking sheets. Bake for 9 to 11 minutes. Let the cookies cook for 4 minutes on the baking sheets and then transfer to racks to cool completely.
For the flour blend: Mix together all ingredients in a large container and store in the refrigerator.