If a project is important or crucial, I never work for more than an hour without saving and completely exiting Storyline. If I get the message you cited, I do a Save As, and give the project a new version number name before I close SL. Deep down, I just know that that message marks the beginning of SL silently corrupting objects in the project. If I can't use that version again, at least I lose only the portion I did since the last version backup.
My favorite saying in the computer world is "There are two kinds of computer users; those who make frequent backups, and those that haven't yet lost important work."