Combine the first five ingredients in the slow cooker.
Cover and cook for 2 to 3 hours on high or 4 to 5 hours on low, until the potatoes are tender.
Mash the soup with a potato masher or blend with an immersion blender. Add the cream. In a medium bowl, toss the cheese with the flour, then stir it into the soup along with the lemon juice. Cook until the soup is heated through, about 20 minutes more. Add the nutmeg, cayenne, and more salt and pepper to taste.
Serve with a sprinkle of chives, croutons, or both, if desired.