In a bowl, add everything except the flours. Mix well for 2 minutes until well combined. Let sit for 2 minutes. Mix again for a few seconds.( to help the flax become gel-ish)
Add the flours and mix using spoon or hand to a dry dough.
Add the chocolate chips and mix to distribute.
Chill the dough for 15 minutes in the refrigerator.
Make flat balls and place on parchment lined baking sheet.
Bake in preheated 350 degrees F for 13-14 minutes.