Hi Samuel and William, I still cannot reproduce the problem consistently and it seems hard to reproduce. Let's try to reproduce it with emacs -Q first, then consider customization later on.
Also, I don't think we can prevent the users from ending up with wrong ellipses in *all* circumstances. `org-catch-invisible-edits' was a step in this direction, preventing users to accidentally delete hidden regions, but it's impossible to catch all mistakes. Let's try to catch the most obvious/disturbing ones first. Thanks, -- Bastien