I've always found connecting to calibre twice works best especially when adding books to collections, basicly I connect the first time do all my book moving and eject then I wait for the reader to stop it's usual checks then connect the second time.
Before I did this I found collections pretty messed up with empty ones etc but now everythings good I can only assume the Sony software fights and messes with the database Calibre loads the first time and accepts the changes the second time.
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