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What you describe is a classic case of (cloudsync race condition ) putting back that which you properly removed/changed with Calibre.
Calibre normally cleans up after itself. An Author without ANY books, say ssomething interfered with the process. Last book to be changed/removed from that Author (as was spelled) , deletes the Author folder.
Same goes for a title rename (your original case). There MAY be an exception because of non-standard usage (Betterread can probably answer), where Auxillary files are store in the Book or Author folders. It might not get deleted as it is NOT Empty (those files). If you do NOT store non-book formats, this should not ever happen
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