Cover beans with 3 inches of water in a medium pot. Bring to a boil. Remove from heat and cover for 1 hour. Drain.
Heat oil in a large pot over medium-high heat. Saute onion, garlic, and red pepper flakes until tender, about 4 minutes. Add collard greens in batches, stirring until wilted. Add beans, Parmesan rind, and water. Bring to a boil. Reduce heat and simmer, covered, until beans and greens are tender, about 1 hour 20 minutes. Season with salt and vinegar.