While the dough is chilling, prepare your filling. In a large pot, stir together the 1 inch chunks of apple, lemon juice, cinnamon, nutmeg, salt, sugars, and vanilla until the apples are evenly coated. Cook the apples on the stove over medium heat, stirring occasionally, for 15-20 minutes until the apples are tender with just a little bite left to them. Whisk together the corn starch and water and pour into the pot with the apple filling. Allow to cook for another minute. Remove the filling from the heat and transfer to a large dish. Cool at room temperature for 30 minutes before transferring to the fridge or freezer to cool completely.