Pre-heat your oven to 375 F. Brown hamburger in large skillet on medium, add chopped onions. Cook until brown and onions are soft. Remove from heat, then add cumin, chipotle, salt, and pepper. Set aside. Prepare 3/4 of the green chilis by slicing down the side so they can be spread out flat on the bottom of a casserole dish or square glass baking pan. Layer the ground beef mixture over the chilis. Top with cheese. Chop the remaining green chilis and layer on top of the cheese. In a medium bowl whisk together the milk, eggs, and then the flour. Pour this mixture over the casserole. Bake in center rack of oven for 35 minutes. Enjoy!