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I have a theory about what is going on here.
Normally Kindles are kept in sync with your Amazon account using a to-do list whenever the device connects to Amazon. That list contains the changes made since the last time the Kindle has interacted with Amazon. Things like book added, book deleted, last page read of a book updated, annotation added, etc.
My guess is that when a device fails to connect for as long period of time the to-do list is scrapped and a different procedure is used to synchronize the device once it finally connect to Amazon. In that case it seems to be going through the device book-by-book bringing the state of each book up to date.
However there is a potential problem with books sideloaded via calibre. When calibre converts a book to Kindle format it includes internal metadata that makes the book appear to be a purchase from Amazon (cdtetype=EBOK). That metadata enables extra functionality on the Kindle that is not available for personal documents.
I suspect that the cleanup process tries to synchronize these books with the reading position and annotations from the user's account only to find that the book is not actually owned by that user. Rather than just ignoring that and moving on to the next book it seems they have chosen to delete the book instead. Perhaps they justify doing that by considering the user to be making use of Kindle features to which they are not entitled by not actually purchasing the book from Amazon. Or perhaps it was just a bad choice made by a software developer.
A way to test this theory would be to sideload some books that do not include this metadata and see whether they are deleted after a long period in airplane mode.
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