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Originally Posted by waldektroc
Is there any chance to recover missing files?
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Run Check Library (Library button / Library Maintenance / Check library.) The books may be left behind, marked as not in calibre's database. If they are not then they are gone.
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How to prevent such incidents in the future (maybe next fakies are being deleted even right now)?
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I know you don't want to hear this but...
Stop using the NAS. If you don't then you will lose books again.