Pour almond milk into a measuring cup. Mix in apple cider vinegar and ground flax seeds with a fork. Set aside; mixture will thicken.
Meanwhile, in a large mixing bowl, sift together flours, baking powder, spices and salt. Create a well in the center and add the milk mixture and the apple sauce, apple juice, vanilla and maple syrup. Use a fork to mix until relatively smooth, a few lumps are okay. Let the batter rest, and preheat a large, non-stick or cast iron pan over medium heat.
When pan is hot, spray with a thin layer of cooking spray and use an ice cream scooper or scant 1/4 cup measure to pour batter and form pancakes. If you can fit three at a time that’d be great. The pancake should start to form little air bubbles, but not as much as pancakes with oil do, so don’t worry if they don’t bubble too much. Cook until the edges are dry and the tops of the pancakes are only slightly wet, about 2 1/2 to 3 minutes, then flip and cook for 2 minutes more. Keep warm on a plate covered with tin foil until all pancakes are ready to serve.
Serve hot with apple topping.