When you make changes to a prefab, the changes will not be applied to any instance of that prefab instantiated at runtime until you close/reopen the project.

NOTE: I've only been able to reproduce this with prefabs created with the legacy prefab system and then upgraded. Prefabs created with the new system don't suffer from this problem.

1. Install Unity
2. Open the attached project (prefabupgraderepro.zip)
3. Open SampleScene.scene
4. Find "LegacyPrefab" in Project View and open it
5. Make some changes to the prefab
6. Save the prefab and return to Scene view
7. Enter Play Mode
8. Investigate the instance of LegacyPrefab that is instantiated

Result:
The prefab instance doesn't have the changes made to the root prefab applied to it.

Expected Result:
The changes made to the prefab should be applied to the instantiated prefab instance.

Found in 2018.3.0a6