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What version of PHP are you using? If it's very new there could be a problem.
Maybe you could try to reinstall cops, apache2 and all dependencies as a last possible solution.
How did you copy the Calibre (what version on Win, OSX or Linux?) database files to your pi?
Maybe first zip, then copy then unzip.
I vaguely remember a problem with something like this once. Or it could be totally unrelated. Just trying to help another cops user. :-)
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