Preheat oven to 325 degrees F (165 degrees C). Spray 2 baking sheets with cooking spray.
Whisk oats, pastry flour, flax meal, cinnamon, salt, and baking soda together in a large bowl. Stir honey, egg whites, almond butter, and vanilla extract into oats mixture until dough is well-blended; mix in chocolate chips. Scoop dough into 36 balls and place on prepared baking sheets.
Bake in the preheated oven until lightly golden and set, 8 to 10 minutes. Cool on the baking sheet for 10 minutes, lightly loosen each cookie from the baking sheet, and continue cooling on the baking sheets for another 10 minutes.