Preheat oven to 300 degrees F. Line two baking sheets with parchment paper; set aside. Heat a large saucepan over medium heat. Combine apple juice, pumpkin, honey and oil in the pan, bring to a simmer. Remove from heat. Stir in oats and wheat germ. Allow mixture to cool slightly. Stir in whole wheat flour and cinnamon. Stir in the all-purpose flour. Divide dough in half.
On a lightly floured surface, roll half the dough at a time into a 10x10-inch square. Using a pastry wheel or knife, cut dough into 2-inch squares. Place squares close together on the prepared baking sheets.
Bake on separate oven racks for 45 minutes, rotating sheets halfway through baking. Turn oven off; let dry overnight. Transfer treats to two 1-quart containers. Store in the refrigerator.