Preheat oven to 350 degrees F. Line a baking sheet with parchment paper.
In a small saucepan, combine the apples, 2 tablespoons pure maple syrup, and 1 teaspoon cinnamon. Cook over medium-low heat, about 10 minutes, until apples have softened.
Meanwhile, in a large bowl, stir together oats, oat flour, flaxseed, 1 teaspoon cinnamon, nutmeg, baking soda and salt. Set aside.
In a medium bowl or measuring cup, whisk together the applesauce, honey or maple syrup, egg and vanilla. Whisk in the melted butter.
Pour the wet ingredients into the bowl and with the dry and stir until combined. Fold in the cooked apples and their syrup.
Scoop rounded 1/4 cup portions of dough onto the prepared baking sheet, using your hands to shape the dough into uniform balls as needed. Gently flatten each cookie a bit as they won't flatten on their own during baking. Bake for 12-14 minutes until the cookies are set and lightly golden.
One completely cooled, cookies can be stored in an airtight container in the freezer for up to 2 months.