Cover sauerkraut with cold water by 1 inch in a large bowl and soak 5 minutes, then drain in a colander. Repeat soaking and draining once more, pressing on sauerkraut.
Preheat oven to 325°F.
Peel and core apples and cut into 1/4-inch-thick slices.
Cook shallot and onion in butter in a 4- to 5-quart pot over moderate heat, stirring, until softened, 8 to 10 minutes. Add apples, bacon, wine, broth, thyme, juniper berries, and bay leaf and bring to a simmer, then stir in sauerkraut. Cover pot with foil, then lid, and braise in middle of oven until tender, 1 to 1 1/2 hours. Discard bay leaf.
Meanwhile, simmer cream and schnapps in a 2-quart saucepan until reduced to about 1 cup, about 40 minutes.
Add cream mixture, salt, and pepper to sauerkraut and stir well.
Available at many supermarkets and Penzeys Spices (800-741-7787).
