In a small bowl, mix the ground flax seeds with the water. Stir, and set aside. After 10 minutes, it will form into a gel.
In a medium bowl, combine the soy milk with the apple cider vinegar. Stir, and set aside.
In a large bowl, combine the all-purpose flour, whole wheat flour, baking powder, coconut sugar, cinnamon, and salt.
Stir in the flax mixture, soy milk mixture, melted butter, and vanilla, until a thick batter forms.
Heat up the waffle iron to medium-high heat. Spray both sides with cooking spray. Pour in ¾ cup of the batter, close the waffle iron lid, and cook for 4 to 5 minutes. Remove and place the waffle on a cooling rack, repeating the process with the remaining batter.