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What version of calibre are you using?
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Latest version 0.7.10, started on 0.7.09. On reflection, the calibre update could have been in the middle of all this.
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Do you backup your library and metadata.db file on a regular schedule?
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Not at the moment, I am still (trying) to build my library - I have something over 2000 books to import so regular backups while I am doing it are a bit difficult. I was thinking of picking up a Python manual and knocking together a backup facility with the 7-Zip libraries.