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I'm sorry, but I am stumped...
Perhaps time for a full reset? Brute Force!
I suggest that you make a backup of all your books.
Then uninstall calibre and delete all calibre library folders.
After that reinstall latest calibre fresh. Now you are sure everything is OK!
Start to carefully add ONE of the books from the backup copy to the new fresh calibre library.
Experiment with settings and patterns for the import until everything works correctly. Then add the rest.
... or wait for other suggestions ...
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