Preheat the oven to 350 degrees F and coat 4 cups of a muffin pan with cooking spray. Fold each tortilla in half, then form into a cone, overlapping the sides. Fold up the point of the cone slightly, then press the tortilla into the prepared muffin pan to form a cup shape; coat with cooking spray. Transfer to the oven and bake until golden and crisp, about 15 minutes.
Meanwhile, combine the flour, cumin, chili powder, 1/2 teaspoon salt and a few grinds of pepper in a large bowl. Add the chicken and toss to coat.
Heat the olive oil in a large nonstick skillet over medium-high heat. Add the chicken in a single layer and cook, stirring occasionally, until lightly browned, about 2 minutes. Add the onion, celery, carrots and bell pepper and cook until the vegetables begin softening, about 2 minutes. Add the tomatoes and chicken broth to the skillet and bring to a simmer. Cook until the vegetables are tender and the sauce thickens slightly, about 5 minutes. Stir in the cilantro and season with salt and pepper.
Divide the chicken mixture among the tortilla cups. Top with the cheese.