Preheat oven to 350 degrees. Coat a large baking dish with cooking spray.
Make the flax egg by mixing the flaxseed and water together in a small bowl. Set aside.
In a mixing bowl, whisk together the flours, baking powder, pumpkin pie spice and salt.
In another mixing bowl, whisk together the melted coconut oil, melted butter, almond milk and sugar. Add in the pure pumpkin, vanilla, and flax egg, then mix together again.
Pour the flour mixture into the wet mixture in two batches, mixing together well. Fold in the chocolate chips.
Pour the batter into the baking dish, spreading out evenly. The mixture should be somewhat thick.
Bake for 25 minutes, or until the bars are lightly browned and pass the toothpick test.
Allow them to slightly cool before cutting into bars.