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Preheat oven to 400 F.
Prepare the butternut squash. Slice each one in half lengthwise. Keep fingers away from the knife to avoid injury. Use a spoon to scoop out the seeds and fleshy strands tangled with the seeds.
Place butternut squash cut sides up on a baking sheet. Drizzle the cut sides of butternut squashes with olive oil and rub the oil into the squash. Season generously with salt and pepper. Turn the squash over, and place it cut sides down on a baking sheet. Tip: you can line the baking sheet with parchment paper for easy clean-up.
Roast in the preheated oven at 400 F for 40 minutes.
While the butternut squash is roasted, prepare the cheese mixture.
In a medium skillet, heat olive oil on medium heat and add fresh spinach. Cook for about 5 minutes until the spinach wilts. If there is any liquid in the pan, drain it.
Add cream cheese to a microwave-safe large-sized bowl. Soften cream cheese briefly in the microwave oven. Make sure the cheese does not actually melt, just softens.
Add shredded Parmesan, cooked spinach, and half of the chopped cooked bacon to the same bowl. Mix everything well. Tip: save the remaining half of the bacon pieces to arrange on top of the cheese mixture.
By this time, you have roasted the butternut squash for 40 minutes. Remove it from the oven and turn cooked squash halves cut sides up.
Let it cool slightly. Using a spoon, scoop out the flesh leaving about a 1-inch border along the sides. (For reference, I provide the step-by-step photos, including for this step, above the recipe card).
Divide the spinach, bacon, and cheese mixture among the 4 halves and stuff the squash until the mixture is leveled. Top with the remaining chopped cooked bacon.
Roast the stuffed butternut squash in the preheated oven at 400 F for 15 more minutes until the cheese mixture melts.
Optionally, broil for 3 or 5 minutes to get golden crust over cheese. Watch closely and be very careful not to burn the squash and the cheese mixture. Tip: Broil on the second oven rack from the top - not on the very top rack so that it doesn't burn. Do watch carefully because all ovens are different. My squashes were fine broiled for 5 minutes on the second oven rack from the top.
Top with freshly ground black pepper and fresh thyme.