In a large saucepan, simmer squash and onion in vegetable stock until very soft.
Place cooked squash and onion in a blender and add enough of the cooking liquid to cover by 2-inches. Blend until smooth. Season with salt, pepper, and nutmeg, to taste. Add truffle oil. Blend a moment until oil is incorporated.
Remove puree from blender into saucepot and stir in enough of the remaining liquid to achieve desired consistency.
Place all ingredients in a stockpot and simmer 2 1/2 to 3 hours.
Strain and return liquid to pan. Reduce over medium-high heat to 4 cups.