That is what it means, If the movie in your library is not on one of your lists it will be removed from radarr and the file will be deleted from disk.
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I'm really sorry for reiterating this, but what you wrote also implies that movies that weren't on any list will also be deleted (don't want that), along with the movies that were on a list and now aren't (do want that). do you have first-hand experience with this?
That’s how it works. I don’t think many people use the option.
If it helps, you could choose the keep and unmonitor option, and then once you’ve confirmed that it does indeed impact movies not on your lists (by unmonitoring them), you can disable the cleaning option (or choose a better option for you) and update all your movies back to Monitored.