Preheat the oven to 400° F. Slice off the top and bottom from the butternut squash; slice in half lengthwise and scrape out the seeds and pulp with a spoon. Peel the squash with a potato peeler, and chop the squash into 1" cubes. Toss in a little olive oil, lightly salt and spread on a baking sheet. Roast until very, very soft and lightly caramelized, about 30 minutes.
In a large pot, melt the butter over medium high heat and cook until lightly browned. Lower the heat and add the remaining olive oil and the onion. Saute until the onion begins to caramelize - about 20 minutes.
Add the squash, water, apple cider, and salt to the pot, and bring to a simmer for 10 minutes to mingle the flavors.
Pour the soup into a blender and puree to a smooth, silky soup. See Cook's Notes for tips.
Pour the pureed soup back into the pot and reheat. Correct seasoning if needed before serving.