Preheat your oven to 375°F (190°C) and lightly grease a 9x13-inch baking dish so the enchiladas do not stick.
Warm 1 cup of the red enchilada sauce in a small saucepan or microwave-safe bowl until just heated through, then spread about 1/3 cup of this warmed sauce over the bottom of the prepared baking dish to create a thin, even layer.
Heat the olive oil in a large skillet over medium heat, then add the finely chopped yellow onion and cook, stirring occasionally, for 4 to 5 minutes until the onion is softened and lightly translucent.
Add the cooked shredded beef brisket to the skillet with the onion and stir to combine, allowing the brisket to warm through for 2 to 3 minutes while gently breaking up any larger pieces with a spoon.
Season the brisket mixture by sprinkling in the ground cumin, chili powder, smoked paprika, garlic powder, fine sea salt, and black pepper, then stir well and cook for another 1 to 2 minutes so the spices bloom and coat the meat evenly.
Remove the skillet from the heat and stir in the sour cream, 2 tablespoons of the chopped fresh cilantro, and the fresh lime juice until the mixture is creamy and well combined; taste and adjust the seasoning with a pinch more salt or pepper if needed.
Lay the flour tortillas on a clean work surface and divide the brisket filling evenly among the 12 tortillas, placing a line of filling down the center of each one.
Sprinkle 1 cup of the shredded Mexican blend cheese evenly over the brisket filling in the tortillas, reserving the remaining 1 cup of cheese for topping.
Working with one tortilla at a time, roll it up snugly around the brisket and cheese filling, then place each rolled tortilla seam-side down into the sauced baking dish, arranging them in a single layer.
Pour the remaining 1 cup of red enchilada sauce evenly over the rolled tortillas in the baking dish, making sure each enchilada is lightly coated with sauce.
Sprinkle the remaining 1 cup of shredded Mexican blend cheese evenly over the top of the sauced enchiladas to create a generous cheesy layer.
Cover the baking dish loosely with foil, tenting it slightly so it does not stick to the cheese, and bake in the preheated oven for 15 minutes to heat everything through.
Remove the foil and continue baking for an additional 10 to 15 minutes, or until the cheese on top is fully melted, bubbly, and lightly golden around the edges.
Carefully remove the baking dish from the oven and let the brisket enchiladas rest for 5 to 10 minutes so the filling can settle slightly, then sprinkle the top with the remaining chopped fresh cilantro and the sliced green onion before serving.