Steps to reproduce:

1. Open attached project
2. Open scene "Scenes/TransparencyBugScene"
3. In top menu, open "Ninjetc Tools > PixelDestruction > New Terrain" menu
4. Select the bottom option "!!! Delete Existing World !!!"
5. Save the scene but not as new scene
6. Re-open scene - notice that deletion of objects isn't saved

Workaround: Instead of DestroyImmediate, use Undo.DestroyObjectImmediate

Not reproducible: 5.2.4f1, 5.3.0a3
Reproduced with: 5.3.0a4, 5.3.4p2, 5.4.0b14
Regression introduced in: 5.3.0a4