Preheat oven to 350°F. Lightly coat a large sauté pan with olive oil over medium heat. Add onion and cook until softened, 1-2 minutes. Add butternut squash and corn, sautéing for 3-5 minutes. Add beans, green chilies, cumin, chili powder, salt, and pepper, cook for an additional 3 minutes, stirring often.
In a 12x9 glass baking dish, spread one cup of the salsa verde evenly on the bottom. Fill each tortilla with about ½ cup of filling, add 2 Tablespoons of shredded cheese, roll tightly and place seam-down in the baking dish. Repeat for the remaining tortillas.
When all enchiladas are in the dish, top with the remaining salsa to prevent cracking and sprinkle with remaining cheese. Cover with foil and bake for 30 minutes, until the cheese is melted, remove the foil for the last 5 minutes and let cook until lightly browned. Let cool for 5 minutes and serve with cilantro garnish.