Preheat oven to 350 degrees. Spray a 9 x 13 baking dish with oil.
Place oil in a skillet and heat to medium. Add onion and cook for 5 minutes. Add garlic, chilies and chipotle chile powder cook for three minutes longer Whisk in the flour and cook for another 2 to 3 minutes, whisking often to avoid burning. Slowly add in chicken broth, whisking until the mixture begins to boil. Stir in milk and salsa and cook at a simmer for 8 minutes. Remove from heat and stir in cilantro.
Spread ½ cup of the sauce in the bottom of the prepared dish. Top with 4 of the torn tortillas.
In a large bowl combine chicken, quinoa, yogurt (or sour cream) and 1 cup of cheese. Spread ½ of the mixture over the tortillas and top with half of the remaining sauce and tortillas. Sprinkle with 1 cup of cheese. Spread remaining chicken mixture and top of the tortillas and top with the remaining tortillas and then sauce. Sprinkle with remaining cheese.
Bake for 30 to 35 minutes. Allow to rest for a few minutes and serve warm. May be made ahead and refrigerated prior to cooking or frozen for up to one month.
Note: When using Greek Yogurt in place of sour cream, I like to place it in a fine metal strainer set over a bowl for about an hour. (You can also place it in the fridge overnight.) This allows some of the liquid to drain off and prevents the casserole from getting runny.