After making changes to a prefab in the project window those changes are not updated in any nested prefabs.
When modifying a prefab directly in the project window it is necessary to save the prefab first in order to propagate those changes. This can be done by either saving the scene or saving the project.
The reason for this is that Unity does not immediately save changes made to a prefab in the project window and therefore Nested Prefabs won't know that any changes have been made. Saving the scene or project will write the prefab changes to disk and Nested Prefabs will be able to properly process them.