Add the almond flour, coconut flour, xanthan gum, baking powder, and sea salt to a medium bowl and whisk until well combined.
Place the shredded mozzarella cheese and cream cheese in a microwave safe bowl and heat in short bursts, stirring between each, until fully melted and smooth.
Quickly add the beaten egg to the warm cheese mixture and stir until mostly incorporated, then add the dry flour mixture and knead with a spatula or clean hands until a smooth dough forms.
Form the dough into a disc, wrap it in plastic or parchment, and let it rest at room temperature for about 10 minutes to reduce stickiness and improve elasticity.
While the dough rests, heat the olive oil in a large skillet over medium heat and add the minced onion, cooking until softened and translucent.
Add the ground beef to the skillet and cook, breaking it apart with a spatula, until browned and no longer pink, then drain off any excess grease if needed.
Stir in the minced garlic, ground cumin, smoked paprika, dried oregano, black pepper, and salt and cook until fragrant, about 1 minute.
Pour in the beef broth and simmer briefly, stirring, until the liquid is mostly reduced but the mixture is still moist, then remove the skillet from the heat and let the beef cool to lukewarm so it does not melt the dough.
Once the beef has cooled slightly, stir in the shredded mozzarella and cheddar cheeses until evenly distributed, then taste and adjust seasoning with more salt or spices if desired.
Cut a large sheet of parchment paper and place the rested dough between two sheets of parchment, then roll it out to about 1/8 inch thickness, making sure it is an even layer without cracks.
Use a round biscuit cutter or small bowl about 4 inches across to cut circles from the dough, gathering and rerolling scraps as needed to make about 8 circles.
Place a dough circle on a piece of parchment, spoon a small amount of beef and cheese filling onto one half of the circle, leaving a border, and lightly moisten the edge with a bit of egg wash.
Fold the dough over the filling to form a half moon, press the edges together firmly with your fingers to seal, then crimp the edge all around with the tines of a fork to reinforce the seal and create a decorative border.
Repeat with the remaining dough circles and filling until all empanadas are formed, setting them on a parchment lined baking sheet as you work.
Brush the tops of the empanadas lightly with the egg wash, making sure not to soak the seams so the seal stays strong.
Preheat the air fryer to 350°F and lightly brush the basket or a piece of parchment cut to fit with olive oil to prevent sticking.
Arrange a single layer of empanadas in the air fryer basket with a little space between each one so air can circulate well, working in batches if necessary.
Air fry the empanadas at 350°F for 8 to 10 minutes until deeply golden and crisp on the outside, then carefully turn them and cook for another 4 to 6 minutes until the crust is firm and the filling is hot and melty.
Transfer the cooked empanadas to a wire rack to cool for a few minutes so the crust sets and the filling thickens slightly before serving.
Garnish the empanadas with chopped fresh cilantro or parsley if desired and serve warm with keto friendly dips such as guacamole, spicy mayo, or sour cream.