Slice chiles in half and remove seeds. Arrange half of the chiles in a greased 13x9-in. baking dish. Sprinkle with shredded cheddar cheese. Cover with remaining chiles. In a small bowl, whisk the eggs, milk and flour until smooth; pour over cheese. Bake, uncovered, at 350° for 30 minutes.
In a small bowl, combine tomato sauce and taco seasoning; pour over casserole. Carefully place cheese cubes on top in a checkerboard pattern; bake 10-15 minutes longer or until top is set. Let stand for 10 minutes before serving.
Wear disposable gloves when cutting hot peppers; the oils can burn skin. Avoid touching your face.