Preheat oven to 300 degrees F. Line two cookie sheets with parchment paper; set aside. In a large saucepan heat and stir apple juice, pumpkin, honey, and oil until mixture simmers. 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 of the dough at a time into a 10X10-inch square. Using a pastry wheel or knife, cut dough into a 2-inch squares. Place squares close together on the prepared cookie 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 canning jars. Store in the refrigerator for up to one week.