Steps to reproduce:
1. Open the "Pumping Plant Level" Unity Project
2. Start the "CANNOT DELETE PUMPING STATION" scene
3. Delete the Prefab "Pumping Station"
4. Save the Scene
5. Reopen the same Scene by double clicking on it in the Hierarchy

Expected result: Prefab is deleted from the Hierarchy
Actual result: Prefab reappears in the Hierarchy after reopening the Scene

Reproducible with: 2017.4.17f1, 2018.2.19f1, 2018.3.0f1, 2019.1.0a11

Note: this is related to Unity not being able to create an Undo Object. If all other programs are closed (memory is not overloaded) it is possible to delete a large Prefab like this. Because of the memory limitations, having such a big Prefab Asset will sometimes cause a crash on loading the Project in Unity Releases 2017.4-2018.2.