Heat oven to 375° F. Divide the squash and shallots among 2 large rimmed baking sheets. Toss the vegetables with a total of 2 tablespoons of the oil and season with a total of ½ teaspoon salt and ½ teaspoon pepper. Arrange in a single layer and roast, turning once, until golden brown and tender, 50 to 55 minutes.
Meanwhile, simmer the cider in a small saucepan until reduced to ¼ cup, 12 to 15 minutes. Let cool for 5 minutes. Whisk in the vinegar, mustard, parsley, the remaining 2 tablespoons of oil, and ¼ teaspoon each salt and pepper.
Transfer the squash and shallots to a serving dish and drizzle with the vinaigrette.