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One possibility that occurs to me is that some Kindles may have particularly inaccurate internal clocks that drift over time. When they do eventually connect back to Amazon the Kindle's clock may be so far out of sync with the actual time that the timestamps of changes made while the Kindle was offline cannot be trusted.
That could be triggering an extreme synchronization mechanism meant to bring the Kindle back in sync with the state of books in the user's account. And that mechanism may be what is deleting sideloaded books, specifically those whose internal metadata indicate that they were Amazon purchases, as those produced using calibre typically are.
Perhaps someone who has experienced this problem in the past and has had their Kindle in airplane mode for weeks since then could check what time their Kindle shows to see if the clock has drifted since it lasted connected to Amazon.
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