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You may have sent multiple copies of the same book to Amazon during your testing. And so your 3 devices are not always working on the same book or document.
It may be worth deleting all copies of the problem titles from clouds and devices then resending a new calibre conversion once you are sure that all previous ones have been removed.
AFAIK the cloud does not try to manage or overwrite duplicates. Each item you send is added to the cloud collection, as if it is a new book, even when it is not.
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