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I am not going to be fixing this in calibre. As I have explained elsewhere metadata.db is *private to calibre*. Third party applications should not rely on it being unchanged. If an application such as calibre sync wants to use metadata.db then it is very much on it to ensure it handles changes to the database schema. Indeed given that calibre sync appears to be unmaintained, I would discourage anyone from relying on it since as metadata.db and other parts of calibre change over time, it is quite likely calibre sync will either break or worse corrupt data.
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