In a medium saucepan set over medium-high heat, combine the sugars, cornstarch, vanilla, cinnamon, nutmeg, and salt. Stir in the water and bring to a simmer. Simmer, stirring constantly, for 2-3 minutes, or until the mixture is thick and lava-like. Stir in the apples and cook 8-10 minutes, or until softened. Let cool completely.
Pour off about 1/4 cup of the liquid from the apples and stir it into the cream cheese.
Heat the oven to 350ºF and line a baking sheet with parchment paper or a silpat.
Use a rolling pin to gently stretch each disc of empanada dough slightly, then spoon 1 tablespoon of cream cheese and 1 heaping tablespoon of apples onto the center of each disc. Bring the edges together over the dough and use the tines of a fork to seal (press firmly). Arrange on the baking sheet. Brush each empanada with milk and sprinkle with cinnamon-sugar, if desired.
Bake 20-25 minutes, or until the empanadas are puffed and golden brown.
Serve hot or at room temperature.