Place beans in a soup kettle or Dutch oven; add water to cover by 2 in. Bring to a boil; boil for 2 minutes. Remove from the heat; cover and let stand for 1 hour.
Drain and rinse beans; discard liquid. Return beans to the pan; add 10 cups water. Bring to a boil Reduce heat; cover and simmer for 30 minutes. Drain, reserving 1/2 cup liquid.
Line the bottom of a 4-qt. baking dish with bacon. In a large bowl, combine the beans, onion, salt and mustard. Spoon over bacon. Pour syrup over the top. Cover and bake at 350° for 3 hours, gently stirring occasionally and adding reserved bean liquid if needed.
Arrange sliced apples over the top. In a small bowl, cream butter and brown sugar; spread over apples. Cover and bake 1 hour longer or until beans are tender.