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This has happened with my Clara several times. I have 2 libraries in one instance of Calibre. What I noticed was that if I switch libraries with the Clara connected, add books from both and then disconnect, it resets or corrupts the BookReader.sqlite database.
It seems that some settings can be different in each library, even though there's one instance of Calibre. I have been going through all the settings and making changes so they match. Also, I have not switched libraries when connected. So far the corrupted database error and resets have stopped.
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