In a large pot over medium heat, cook and stir the bacon with the annatto seeds until the bacon pieces are browned, crisp, and colored from the seeds. Stir in onion, garlic, 1/2 cup parsley, and 1/4 cup cilantro; cook and stir the vegetables in the bacon drippings until the onion is translucent, about 5 minutes. Add the beans, oregano, cumin, kosher salt, pepper, lime juice, and bay leaves. Pour in enough water to cover the beans by about 4 inches, and bring to a boil over medium heat.
Cover the pot and simmer the beans and seasonings until tender, about 3 hours, adding water if necessary to prevent burning. Stir in the olives and 1/4 cup cilantro, and simmer for 30 more minutes, uncovered, to reduce excess soupiness if desired. Sprinkle with 1 teaspoon or more of fresh parsley, and serve.