Put butternut squash in a large stockpot and fill with enough water to cover the squash. Bring water to boil, and cook until squash is soft, when pierced with a fork about 20 minutes. You may need to rotate the squash from time to time to ensure even cooking.
Meanwhile, in a medium skillet heat oil over medium-high heat. Saute onions until soft. Add garlic, chipotle, and adobo sauce. Saute until fragrant, another minute or two more.
Remove the squash and cut in half lengthwise, and scoop out seeds. Cut squash into 1 inch or smaller cubes and add to a large bowl. Add onion mixture, ground beef (if using), black beans, cream cheese, cumin, and green onions. Stir well.
Line a 9×13 baking dish with wax paper. Spread 1/3 of the enchilada sauce on the bottom of the dish and spread into a thin layer.
Scoop about 1/4 cup of filling into each tortilla and loosely roll. Place seam side down in the baking dish. Cover with plastic wrap and then foil. Freeze. For best results, remove dish after freezing overnight, enchiladas will easily pop out and can be moved to a vacuum sealed bag with FoodSaver® FM3941 to keep it fresh even longer.
To use FoodSaver® FM3941, turn the lever to open and pull out the roll to measure out how long the casserole is making sure to leave roughly 4 inches of space. Turn the lever to closed. Press the seal button and when the light turns off, cut the bag.
Place the frozen enchiladas inside the bag, make sure the bumpy side on the sheets are on the top.
Slide the open end into the opening and press vacuum seal.
This will be noisy for a few seconds and you will see all the air get sucked out. Then it will seal it and you can pull it out and freeze it. Be sure to label it with what it is, what temperature to cook it at and for how long.
Follow the same steps to vacuum seal remaining enchilada sauce separately and freeze.
On the day before you want to cook, remove the frozen dish and set in the refrigerator to thaw overnight. On Cooking Day: Preheat oven to 350 degrees.
Remove enchiladas from FoodSaver® sealed bag and put into 9×13 dish. Spread thawed enchilada sauce evenly over enchiladas, cover with foil. Bake for 15 minutes in preheated oven.
Remove foil and top with cheese. Cook for 15 more minutes or until cheese is melted, enchiladas are warmed through and bubbly.