Cover beans with water in a large pot and allow to soak for 6 to 8 hours. Drain and rinse under cold running water.
Cover soaked beans with fresh water about 3 inches above the top of the beans and bring to a boil over medium-high heat. Add bay leaf and 1/2 of the bouillon cube. Reduce heat and simmer until beans are al dente, about 45 minutes.
Drain beans and reserve the liquid. Discard bay leaf.
Heat olive oil in a large pot. Add onion and bell pepper; cook until soft and translucent, about 5 minutes. Add drained beans and stir to combine. Add remaining 1/2 bouillon cube, tomato sauce, tomato paste, sugar, mustard, vinegar, chipotle flakes, and paprika. Stir and simmer until sauce has cooked down and beans are soft but not mushy, about 20 minutes. Add some of the reserved bean stock if necessary to keep it from burning, but not too much to make it soupy. Serve warm.