Place lima beans in a large pot with enough water to cover by 2 inches; bring to a boil. Remove pot from heat and let stand for 2 hours. Drain and rinse beans under cold water.
Transfer beans back to large pot and pour in enough water to cover; add sausage and red pepper flakes. Bring water to a boil, decrease heat, and simmer, adding water as needed to keep beans from sticking to the bottom, until beans are tender and liquid has thickened, 1 to 2 hours.