Place cheeses and cornstarch in a zip-top bag and shake until well coated.
Bring apple juice to a simmer over medium heat in a heavy 5-quart pot. Whisking constantly, slowly add cheese mixture 1/2 cup at a time until smooth and fully incorporated. (Let mixture come to a simmer again after adding each 1/2 cup cheese.) Remove pan from heat and whisk in mustard, nutmeg, and three-fourths of bacon.
Serve in a small slow cooker on warm or a fondue pot set over a sterno flame. Garnish with remaining bacon. Serve with desired dippers and a skewer for each guest.