In a medium bowl, whisk together the eggs, almond milk, applesauce, and vanilla.

In a food processor, place the all-purpose and whole wheat flours, the sugar, baking powder, cinnamon, salt, and nutmeg pulse to combine. Add the hardened coconut oil and pulse a few times until the coconut oil is just combined.

Transfer the mixture to a large bowl and stir in the apple. Add the egg mixture and use a spatula to fold until the dough just comes together. Be careful not to overmix.

Turn the dough out onto a floured surface. Knead lightly, using more flour as needed to prevent sticking. Form the dough into a ball, divide it in half, and flatten each half into a 1-inch-thick disk. Place on a parchment-lined baking sheet and freeze for 20 minutes.

Preheat the oven to 400°F and line another baking sheet with parchment paper.

Remove the dough from the freezer and cut each disk into 6 wedges. Separate the wedges and arrange them on the prepared baking sheet. Bake for 15 to 17 minutes, or until golden brown around the edges. Transfer to a wire rack to cool.

Make the glaze: In a medium bowl, whisk together the powdered sugar, almond milk, and vanilla until smooth. Drizzle over the cooled scones. If desired, sprinkle the glazed scones with chopped pecans.

Store in an airtight container at room temperature for up to 3 days or freeze for up to 3 months.