Preheat the oven to 300 degrees F.

In a heavy ovenproof cast iron Dutch oven, cook the bacon over medium-high heat until rendered and crispy, 4 to 6 minutes. Add the onion and cook, stirring, until softened and lightly caramelized, 3 to 4 minutes. Add the garlic and thyme and cook for 1 minute. Add the beans, coffee, barbecue sauce, brown sugar, mustard, molasses, hot sauce, and pepper and stir to combine well. Add the water and salt and increase heat to bring liquid to a boil. Cover the pot and place the pot in the oven and cook for 2 hours, undisturbed. Remove the pot from the oven, uncover and stir the beans. Recover the pot and continue to bake until the beans are tender, about 1 hour longer.

When the beans are tender, remove the cover and continue cooking, uncovered, until the cooking liquid has reduced to a thick, sauce-like consistency and beans are thick and flavorful, 1 to 1 1/4 hours longer. Remove from the oven and discard the thyme stems. Adjust seasoning, if necessary, and serve the beans either hot or warm.