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theducks thanks for the quick response!
I mean the directory /home/foo/.config/calibre/ where Calibre stores its configuration files. I cannot see the libraries which I had on B any more. Also my plugins are gone. Calibre has apparently replaced the configuration of B from A. Can I do something about it now? Have I lost all columns and metadata I had on B? No, Calibre didn't warn me about replacing these files.
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