Steps to reproduce:

1. Open the attached project
2. Make sure "Test" scene is loaded and "Test_Art" is unloaded, but in manager
3. Modify Test scene with text editor, rename some object on anything
4. Return to focus to Unity, refresh on project folder
5. Dialog appears, that scenes have changed, press Reload.

Actual results: Reload did not managed to reload modified scene, because it was last loaded scene but not the only scene in hierarchy.
Expected results: Scene should be reloaded

Throws warning:
"Unloading the last loaded scene"

Reproduced with: 5.5.4p1, 5.6.2p2, 2017.1.0f3, 2017.2.0b2, 2017.3.0a1