Unroll one of the pie crusts onto a lightly floured surface. Use a 4-inch round cutter to cut the dough into circles. Repeat with the remaining pie crusts. (I got 5 rounds per pie crust.) Combine the scraps and re-roll the dough ball until you get a total of 24 circles.
Arrange the circles on a parchment paper-lined baking sheet and refrigerate while making the filling.
Melt the butter in a small skillet over medium-high heat. Add the onion and season lightly with salt and pepper. Cook until the onion is tender, about 5 minutes. Remove from the heat.
Add the cream cheese to a medium bowl and stir until smooth. Add the ham, Cheddar cheese, mustard, brown sugar, and soy sauce, stirring until combined. Fold in the cooked onions.
Preheat the oven to 425°F. Line 2 rimmed baking sheets with parchment paper. Remove the pie dough circles from the refrigerator. Arrange the dough on a clean surface. Divide the ham mixture evenly between the dough circles, placing in the center of each circle.
Fold the dough over the filling to create a crescent shape. Press the dough down to seal. Use the tines of a fork to press and seal and the edge of the empanada. Whisk together the egg yolk and water in a small bowl. Brush the egg wash all over the tops of the dough. Use the tip of a paring knife to cut 3 slits into each empanada.
Bake the empanadas for 12 to 14 minutes or until the pastry is golden brown and flaky. Remove from the oven and serve.