Preheat oven to 400 degrees. In a large bowl, toss together butternut squash, carrots, onion, thyme, salt, pepper and olive oil. Spread in a single layer on a baking tray and roast vegetables for 40-50 minutes, until butternut squash and carrots are tender (when pierced with a fork or knife, it should come out easily). Transfer roasted vegetables to a large saucepan and add vegetable broth, apple cider, cinnamon, ginger and nutmeg. Heat through. Puree soup using an immersion blender, regular blender or food processor.