Hi there,
Just after updating to Unity 3.5.0f5 my scene that includes an instantiated prefab with serialized values different than parent one is not saved.
To be totally clear, a prefab with a “uLink Network View” component inserted in my scene must have an unique Id, this is done by the assignement wizard. After that the Id is modified and valid and the scene is saved. Reopen the same scene rollback the Id to the previous value.
We can see with an external editor that the value is not modified after the scene has been saved.
If we modified manually this value the scene will save the modification.