Combine the shredded sweet potatoes, onions, eggs and almond flour in a mixing bowl. Season with ½ teaspoon each salt and pepper. Stir well to combine.
Heat enough bacon fat, coconut oil or ghee to measure 1/8 inch in a large heavy skillet over medium heat. Drop ¼-cup scoops of the mixture into the hot skillet, pressing down on the mixture to spread it out (you should be able to cook about 4 latkes at a time). Cook until the bottoms are golden brown, 3 to 5 minutes, then flip and continue cooking for another 3 to 5 minutes. Transfer the latkes to a paper towel–lined tray to drain. Continue with the remaining mixture, adding more fat as needed between batches and scooping out any loose bits of sweet potato, which may burn and become bitter.
While the latkes cook, add the bacon and apples to a separate large skillet. Sprinkle the cinnamon over the mixture. Cook over medium heat, stirring occasionally, until the apples are tender and the bacon is crisp (carefully pour off or spoon out the excess fat as they cook), about 15 minutes. Keep warm over low heat.
Serve the latkes topped with the bacon and apples and garnished with chopped chives.