Adjust an oven rack to the middle position and heat the oven to 300 degrees.

Combine the beans, baking soda, and the larger portion of water in a large saucepan and bring to a boil over high heat. Reduce to a simmer and cook until the beans are tender but still hold their shape, about 20 minutes—at this point, the baking soda has done its job. Drain the beans and rinse them thoroughly in a colander.

Heat the oil in a large oven-safe Dutch oven over medium heat until shimmering. Add the onion and cook until softened and translucent, about 5 to 7 minutes.

Stir in the molasses, brown sugar, soy sauce, mustard, paprika, and pepper. Add the drained beans and the remaining water, then bring the mixture to a simmer.

Transfer the pot to the oven and bake uncovered until the beans are completely tender and the liquid has thickened into a dark, syrupy glaze, about 2 hours. If the liquid evaporates too quickly and the beans look dry, stir in a small amount of extra water.

Stir in the cider vinegar and season with salt and pepper to taste. Serve warm.