Melt 1 tablespoon butter in a soup pot over medium heat. Cook onion for 7 minutes until softened, then stir in ginger for 30 seconds.
Add squash, broth, cider, salt and pepper. Bring to a simmer, cover partly and cook for 20 to 25 minutes until squash is tender.
Meanwhile, melt remaining butter in a large skillet over medium heat. Add apple cubes in one layer and cook for 8 to 10 minutes, turning occasionally, until lightly browned and just tender.
Transfer about one-third of the squash pieces and 1 cup of the broth to a heatproof bowl and puree with an immersion blender. Return puree to the pot with the sauteed apples and vinegar.
Simmer gently for 3 minutes, keeping the remaining squash and apple pieces intact, then divide among 6 bowls.