I have repetitively experienced the same diminishing shelf content issue. In some cases the number of books on a shelf drops to 0, in others the some number less than what I had added.
I've also had duplicate shelves.
Very annoying, but I do use Calibre to sideload books.
From what I have read above I'll have to do some testing with Calibre.
Glad to have found this thread - it's been driving me nuts!
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