Sorry for the late reply!
Properly handling scene saving has already been added for the next version. (cutscene is now reverted before the scene is saved automatically).
This only work for Unity 5.6+ though, since Unity added a nice callback for when scene is about to be saved in version 5.6.
If you want to modify the source code now and add this change and not wait for the next version, please open up CutsceneEditor.cs and:
1) In OnEnable() method add this code in the beginning: