Finely chop the onion and set aside. To prepare the leeks, cut off the white and light green stem just below the dark green leaves. Discard the tough leaves. Split the stalk in half while leaving the root intact. Wash the leeks, carefully separating the layers and letting the water rinse between to remove any dirt. Cut off the root and then chop the leeks into thick slices.
Heat a large, heavy bottom pot over medium heat. Add the olive oil and the chopped onion and leeks. Sauté over medium heat for 4 to 5 minutes until the onions are soft and translucent.
While the onions are cooking, peel and chop the butternut squash and the yam. When the onions and leeks are tender add the minced garlic and sauté for another minute.
Add the vegetable broth and apple cider to the pot and turn up the heat to high. Tie the thyme stems together with twine and add to the pot along with the cinnamon stick. Add the kosher salt and pepper along with the chopped butternut squash and yams.
Heat the soup until it comes to a boil then turn down to low. Let simmer on low, covered, for about 30 minutes until the vegetables are very tender. Add the canned pumpkin and simmer for another 5 to 10 minutes.
After simmering for about 40 to 45 minutes, remove the thyme bundle and cinnamon stick. Taste the broth for seasoning, adding more salt if desired.
To puree the soup, carefully transfer the soup in two to three batches to a high-speed blender. Blend until completely smooth then transfer to a clean saucepan. Alternatively, you can use an immersion blender, although the soup may not be quite as smooth as with the blender.
Check the finished soup for seasoning and adjust if necessary. If you prefer the soup to be thinner, add a bit more vegetable broth or apple juice. If needed, heat the soup back up over medium heat.
If desired, you can serve this soup with a swirl of cream and a sprinkle of cinnamon.
Notes
* Substitute the leeks with the other half onion if desired.