Preheat oven to 375°F (190°C). Lightly grease a 9 × 13 inch baking dish.
Heat olive oil in a large skillet over medium-high. Sauté onion and bell pepper for 3 to 4 minutes until softened.
Add ground turkey. Cook 6 to 8 minutes, breaking it up, until no longer pink and cooked through. Drain excess fat.
Stir in taco seasoning, smoked paprika, cumin, salt, black pepper, black beans, corn, and salsa. Cook 1 to 2 minutes to combine, then remove from heat.
In a large bowl, whisk eggs, milk, cilantro, flaxseed, and the remaining 1/4 tsp salt until uniform and lightly frothy.
Assemble: spread half the turkey mixture in the dish. Top with 16 tortilla quarters, then half the cheese. Add remaining turkey mixture and the final 16 tortilla quarters.
Slowly pour the egg mixture evenly over the casserole. Top with the remaining cheese.
Cover tightly with foil and bake 45 to 55 minutes, uncovering for the last 10 minutes. Bake until the center is set and the custard reaches 160 to 165°F (71 to 74°C). A knife inserted near the center should come out clean.
Rest 10 minutes before slicing.