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Cook onion and bacon in a large skillet over medium-high heat until the onion is starting to brown, 6 to 8 minutes. Reduce heat to medium-low and continuing cooking until the onion is very soft, about 5 minutes more. Stir in bourbon (or 3 tablespoons broth) and cook for 1 minute, scraping up the browned bits. Set aside.
Drain and rinse the soaked beans; transfer to a 5- to 6-quart slow cooker. Stir in 3 cups broth, ketchup, maple syrup (or brown sugar), molasses, dry mustard and chipotle (or chili powder). Spoon the onion-bacon mixture on top of the bean mixture, but don’t stir the two together. (The layer on top helps keep the beans submerged during cooking so they don’t dry out). Cover and cook on High for 6 hours or Low for 8 hours. Stir in vinegar and salt just before serving.