Preheat oven to 350 degrees F (175 degrees C).

In a large skillet over medium high heat, combine the ground beef and onions and saute for 5 to 10 minutes, or until browned; drain excess fat.

Arrange 1 can of the chile peppers on the bottom of a 7x11 inch baking dish. Sprinkle with half the cheese and top with the meat mixture. Sprinkle the meat mixture with the remaining cheese, followed by the next can of chile peppers.

In a medium bowl, combine the eggs, flour and milk, whisking until smooth. Pour this into the baking dish over the chile peppers. Season with salt and pepper to taste.

Bake at 350 degrees F (175 degrees C) for 45 to 50 minutes. Let cool for about 5 minutes before cutting.