Preheat the oven to 400˚F. Line a large baking sheet with parchment paper.
Place the squash halves, cut side down, on the baking sheet. Roast until tender, 25-30 minutes for honeynut squash, or 40-50 minutes for acorn squash. Remove the pan from the oven and flip each squash over so that the cut side is facing up. Set aside (if there’s a lot of liquid on the pan, transfer the squash halves to a clean parchment-lined pan). Increase the oven temperature to 550˚F.
While the squash bakes, make the filling. In a large skillet, melt the butter over medium heat. Add the onion and celery, and season with salt and pepper. Cook, stirring occasionally, until the vegetables start to soften, about 3 minutes. Add the garlic, apple, rosemary, thyme and cinnamon. Cook, stirring, until the vegetables and apples are tender, about 2-3 minutes longer. Pile in the spinach, and cook, stirring, until wilted.
Stir in the quinoa, and season with salt and pepper. Pour in the broth and cook, stirring, until mostly absorbed. Remove the skillet from the heat and add the apple cider vinegar and pecans. Season with more salt and pepper as needed.
Season the squash halves with salt and pepper (if using acorn squash, I like to dot the top of the squash with a few small pieces of butter and drizzle them with a little maple syrup, as acorn squash isn’t quite as rich and sweet as honeynut). Scoop the filling into each squash cavity (an ice cream scoop works great for this), mounding it firmly. Pile the cheese over the filling.
Roast the stuffed squash in the 550˚F oven until the cheese is lightly toasted, about 4-6 minutes.