Steps to reproduce:

1. Open the attached project
2. Open 'delete_me' scene
3. Select the scene in the project tab
4. Delete the scene
5. Click CTRL+S (or File/Save Scene) to save the scene
6. Notice nothing happens (only in 5.3. Earlier versions just re-saves the scene here)
7. Now delete or add some object to the scene
8. Click CTRL+S again
9. Notice the scene gets saved with the same name (delete_me) again

Expected behaviour would be that after steps 5 and 8, the editor would throw a dialog asking where to save the scene as if you were saving a new scene.