@petzi:
Your Calibre library metadata.db appears to need fixing. Calibre > Library Button > Library Maintenance > Check Library. Then, tell it to delete all of the invalid entries it finds.
Do this after you have deleted all of the books.
Quote:
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But actually nothing will happen before I press the ZMI button for “Autovalidate/Generate Current Library…".
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It would be dangerous to automatically do it, since the user may not want to automatically do it. So, it waits to continue. As long as the dialog with the "OK" and "Cancel" buttons is shown, ZMI is waiting for you to approve its next action.
DaltonST