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Position rack in center of oven; preheat to 350°F. Coat a baking sheet with cooking spray or line with parchment paper or a nonstick baking mat.
Process almonds in a blender in 2 batches until finely ground. Transfer to a large bowl and add whole-wheat flour, oat flour, baking powder and salt. Whisk oil, maple syrup, apple juice, almond and vanilla extracts in a medium bowl. Add the wet ingredients to the dry ingredients; stir to combine. Use your hands to knead the dough together; add 1 to 2 tablespoons additional apple juice if the mixture is too crumbly.
Form level tablespoonfuls of dough into balls and place on the prepared baking sheet about 2 inches apart. Gently flatten each ball into a disk, then make an indentation in the center using your thumb or a small spoon. Place a few chocolate chips in each indentation, then cover with 1/4 teaspoon preserves.
Bake the cookies, one batch at a time, until golden around the edges, 15 to 17 minutes. Transfer to a wire rack to cool completely.