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Originally Posted by eXistenZ
Thank you
Davidfor, at last I decided to get Rid of Calibre's preferences folder and starting from a fresh install, I installed only plugins I really use and all seemed to be solved...
...except I tryed to run in debug mode and that (damned) ebook was still in the log, of course it was because it is not Calibre related.
A facrotry reset was too long, so I decided to log off the Aura from my account, an then log on again to create a new DB, now finally I got rid of that "Tvtti i trionfi, carri..." ebook (There is no more sign of it in the logs). 
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Glad to hear it is working.
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By the way, I still use smart shelves
(but disabled every shelf management option in calibre carefulley)
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If it works for you, that's good. I hope Kobo complete it properly. Though, it's going to be a pain to get the calibre shelf management working properly.
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At the end of all, these days of tests gave me an idea for Kobo tools.
As you noticed my DB was nearly 200MB, but it reduces to 12MB when zipped.
Modifying backup routine of Kobo Tools to make it zipping the DB with the rest of stuff to save a lot of space could be a good idea. Or there is some side effect?
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The only side effect would be me having to unzip the file before looking at the database. I'll add an option for "single backup file" or something like that.