Split chiles and remove seeds; dry on paper towels. Arrange chiles on the bottom of a greased 2-qt. baking dish. Top with cheese. In a skillet, cook beef and onion over medium heat until meat is no longer pink; drain. Spoon over the cheese. , In a bowl, beat milk, eggs, flour, salt and pepper until smooth; pour over beef mixture. Bake, uncovered, at 350° until a knife inserted in the center comes out clean, 45-50 minutes. Let stand 5 minutes before serving.