I've also had Calibre randomly delete books on me. Wasn't using any cloud services, just a internal HD. It was very frustrating. I wasn't able to pin down the precise cause, and no one was able to fix the issue.
I now import new books into Calibre, fix the metadata, and export them immediately to my book storage folders. So far this is easy to manage (despite having several thousand books) and reliable. I save fiction by author and nonfiction by subject.
ETA: Were you copying books through the Calibre tools? The one time I was able to catch it in action the problem seemed to happen when I was moving books between Calibre Libraries. That was only 1 of the 10+ books I lost, though.
Last edited by Rbneader; 08-02-2014 at 01:37 PM.
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