Hi there!
I am experiencing this issue as well. I have managed to identify problem – using alt+drag to duplicate a matinee actor or copy/pasting a matinee actor in viewport will cause current level to become corrupted. I have also found that moving a matinee from one level to another will permanently corrupt level as well. editor will allow you to continue working as if nothing has happened, but as soon as you restart editor you will find that your files have been destroyed.