Preheat oven to 375 degrees. Spray a 9 x 13 baking dish with non-stick cooking spray.
In a large skillet brown ground beef with onion over medium high heat. Drain grease. Stir in taco seasoning, water, green chilies, diced tomatoes, and 5 oz enchilada sauce from can. Simmer for 2-3 minutes. Turn off burner.
Pour 2.5 oz enchilada sauce from can into prepared baking dish covering bottom, sides, and corners.
Cut flour tortillas in half. 1st layer (Bottom): Place 7 tortilla halves on top of the sauce in baking dish in an even layer. (They can overlap if needed.) Spread refried beans on the tortillas in baking dish evenly. Spread 1/3 of the meat mixture on top of the beans. Sprinkle with 1/3 of the shredded cheese.
2nd layer (Middle): Place another layer of tortilla halves evenly over the cheese. Place 1/2 of the remaining meat mixture over the tortillas. Sprinkle 1/2 of the green onions & chopped cilantro on top of the meat mixture. Sprinkle with 1/2 of the remaining shredded cheese.
3rd layer (Top): Place final layer of tortilla halves on top of cheese. Place remaining meat mixture over tortillas. Spread rest of enchilada sauce on top of meat mixture. Sprinkle with remaining green onions & chopped cilantro. Top with remaining shredded cheese.
Bake uncovered for 40-45 minutes until heated through, cheese has melted & mixture is bubbly. Let rest for 5-10 minutes before cutting into squares.