Reheat the brisket. Warm your leftover chopped brisket in a covered skillet over medium-low heat with a splash of beef broth until heated through and juicy, about 5–7 minutes. Set aside.
Make the cheese sauce (optional). Melt butter in a saucepan over medium heat until bubbly. Add flour and stir until combined into a paste. Whisk in the milk and bring to a gentle simmer, then slowly fold in the grated smoked cheddar until completely smooth and glossy. Keep warm on low heat.
Make homemade chips (optional). Fry corn tortilla quarters in small batches in hot oil until slightly browned and crisp. Transfer to a rack and season immediately with sea salt.
Preheat oven to 375°F. Line a large sheet pan with foil.
Layer the nachos. Spread a single layer of chips across the pan. Add half the shredded cheese blend, then scatter black beans, corn, and red onion. Add a generous layer of chopped brisket. Repeat with a second layer of chips, remaining shredded cheese, and more brisket.
Bake for 12–15 minutes until cheese is fully melted and chip edges are just turning golden. Rotate the pan halfway through.
Finish and serve. Drizzle warm cheese sauce over the top if using, then add jalapeños, dollops of sour cream and guacamole, pico de gallo, and fresh cilantro. Squeeze lime over everything and serve immediately.