In a 5- to 6-quart nonstick pan over high heat, stir bacon until browned, 3 to 4 minutes. With a slotted spoon, transfer bacon to paper towels to drain. Add oil to pan; when hot, add onion, apple, and garlic. Stir often over medium heat until onion is very limp and beginning to brown, about 20 minutes. Add wine and stir until evaporated, 3 to 4 minutes.
Add potatoes, 1/2 teaspoon salt, and 3 1/2 cups water; bring to a boil over high heat, then reduce heat, cover, and simmer, stirring occasionally, until potatoes mash easily, 25 to 30 minutes.
Meanwhile, in a 1- to 2-quart pan over high heat, boil apple cider until reduced to 1/4 cup, 8 to 15 minutes.
Add milk to potato mixture and, working in batches, whirl in a blender or food processor until smooth. Return to pan over low heat and stir in apple cider, cheese, nutmeg, and salt and pepper to taste. Stir often just until hot, 2 to 3 minutes. Ladle into bowls and top with chives and bacon.