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I guess its vaguely possible that calibre deleted the files.
But its highly probably that files were lost when copying them across a network, between three different operating environments - XP, NAS (NOT supported by calibre) & Ubuntu - using different file systems - NTFS, Ext3/4, and whatever the NAS uses. And probably with lightweight copy programs.
The losses could have occurred in any one or all of the copy operations and what you see now is the cumulative effect.
BR
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