Set a large skillet over high heat with 1 tablespoon oil. Once hot, add the ground chicken and cook, breaking up with a wooden spoon, until crispy and golden brown, about 8 minutes. Season with 1 teaspoon taco seasoning. Transfer the chicken to plate or platter and set aside. Add the remaining tablespoon of oil and stir in the onion, garlic, squash, chayote, jalapeño and corn. Cook until the vegetables have softened and just beginning to brown, about 5 minutes. Season with 1 teaspoon taco seasoning and then transfer to the same plate or platter as the chicken.
Return the skillet over high heat with the butter. Once melted, whisk in the flour and cook for about 30 seconds. Slowly whisk in the chicken stock and milk. Lower the flame to medium and cook until the sauce has thickened. Stir in 1 cup Cheddar and 1 cup Pepper Jack until melted through. Season with the remaining 1 teaspoon taco seasoning and a pinch more of salt. Fold in the cooked chicken, sautéed vegetables, and brown rice until evenly incorporated. Divide the filling among 6 individual ramekins and place on a baking sheet. Set aside.
Preheat oven to 350 degrees F.
To make the crust, pour about 2 inches of vegetable oil in a skillet with high sides over medium-high heat. Once hot, fry the small tortillas, in batches, until golden brown and crunchy about 2 minutes per side. Drain the excess oil and place on a plate lined with paper towels. Continue frying the rest.
To assemble the crust, spread a bit of the refried beans onto half of the tortillas, sprinkle with the remaining cheese, and then sandwich together with the remaining tortillas. So you'll end up with two tortillas sandwiches together with beans and cheese. Place a stack on top of each pot pie, and sprinkle with more cheese on top.
Bake until warmed through, and the cheese has melted, about 10 to 15 minutes. Remove from the oven and let cool slightly before serving. Enjoy!