To reproduce:
1. Open attached project
2. Open scene "ropeWithSpheres"
3. Try to create a prefab out of the "lanternOnLianas" gameobject - unity crashes

I've noticed that if you remove all of the configurable joints, multiselect the links and try to remove their rigidbodies, one of them says that it cannot be removed due to a joint having a dependency. The weird part is that the object never had a joint in the first place and you can remove the rigidbody when selecting it alone. (In this case it's link 4)