To reproduce:
1. Open the attached project.
2. Open sceneA
3. In the hierarchy search field type: bob
4. The scene view turns grey and 2 green boxes will be highlighted
5. Click on the empty space bellow the game objects in the hierarchy pane
6. The text "bob" from the search box will disappear
7. Load sceneB
8. Game objects are still filtered and the scene is still grey