Pour apple cider into a small saucepan.
Simmer over medium heat until reduced from 1½ cups to approximately ½ cup.
Transfer the reduced cider to a heat-safe measuring cup and cool.
Preheat oven to 350°F (175°C).
Grease a 9-inch round cake pan and line the bottom with parchment.
Whisk whole wheat pastry flour, all-purpose flour, baking powder, baking soda, cinnamon, nutmeg, and salt together.
In a separate large bowl, whisk brown sugar and eggs until smooth.
Whisk in applesauce.
Add Greek yogurt and mix.
Slowly whisk in the oil.
Add vanilla.
Whisk in the cooled ½ cup reduced apple cider.
Add dry ingredients to wet ingredients.
Fold gently until just combined.
Transfer batter to the prepared pan.
Smooth the top lightly.
Bake for approximately 30–36 minutes.
Check the center with a toothpick.
Cool in the pan for approximately 15 minutes.
Transfer cake to a wire rack and cool completely.
Whisk powdered sugar, maple syrup, and 1 tablespoon milk together.
Add additional milk by the teaspoon until the glaze is thick but pourable.
Drizzle glaze naturally over the completely cooled cake.
Let glaze set for approximately 15–20 minutes before slicing.