Steps to reproduce:

1. Set up a Cache server
2. Open attached project
3. Connect to the Cache server (Edit -> Preferences -> Cache Server -> Use Cache Server -> Enter the IP address)
4. Reopen the project (the issue is not reproducible for me if the project is not closed and opened again)
5. Expand 'TestPrefab' prefab to see it's child objects and drag the prefab to hierarchy to create a game object
6. Expand the created object and duplicate one of the child objects
7. Click on the root 'TestPrefab' game object and click 'Apply' to apply changes to prefab
8. Notice that the prefab in the 'Project' window is not updated to have that additional child object
9. If you drag the prefab from 'Project' window to hierarchy to make another instance of an object, it does have all the child objects, therefore this is only a visual issue, as the changes actually get applied to prefab