Cut the bacon into small pieces, place in a large Dutch oven, and sauté over medium-high heat until crispy. Remove the bacon from the pan with a slotted spoon to drain on paper towels. Drain off half of the bacon drippings (reserve for another use). Leave the bacon grease to cool a little bit, and then put the onions in the pot and sauté until soft and translucent. If you drop the onions into the blistering hot grease, they will fry and be crispy, not soft and caramelized.
Meanwhile, whisk ketchup, vinegar, brown sugar, sorghum syrup, dry mustard, salt, and pepper in a small bowl. When the onions are soft, pour in the sauce and stir to coat. Cook until bubbling and the sugar is melted. Pour in the apple cider and stir until heated through.
Drop the drained beans into the pot and stir carefully to coat with the sauce. Stir in half the crisped bacon. Bring the pot to bubbling, then lower the heat, cover, and simmer for one hour, stirring occasionally to prevent the beans from sticking. Stir carefully or the beans will break up and become mushy. Near the end of the cooking time, stir in the remainder of the bacon.