Heat oven to 375°F. Place butter in 13x9-inch (3-quart) glass baking dish; heat in oven 5 to 7 minutes or until melted.
Stir cinnamon and nutmeg into melted butter. Add squash; toss to coat. Cover with foil; bake 20 minutes. Meanwhile, in large bowl, mix apples, syrup and vinegar.
Pour apple mixture over squash. Cover; bake 10 minutes. Stir; bake 5 to 10 minutes longer or until squash is tender. Stir before serving and sprinkle with pecans.