Preheat oven to 350. Spray 9- x 11-inch glass baking pan with cooking spray.
Place flour, salt, and cinnamon into a large plastic bag. Add squash, apples, and onions; shake until lightly dusted.
In glass dish, layer 1/2 of squash, apples, and sweet onion. Pour 1/2 cup chicken stock over the top, then sprinkle 1/2 of cheese. Layer with remaining squash, apple, and onions. Pour remaining chicken stock over the top, and cover with foil.
Bake in preheated oven for 40 minutes.
Take out and sprinkle with bacon crumbles and remaining cheese. Return, uncovered, to oven; bake for another 5 minutes. Let sit for 5 minutes before serving.
