Calibre 9.3.1 incorrectly reports database is corrupted

[Boilerplate4U]

When starting Calibre 9.3.1 on macOS 15.7 Sequoia, it incorrectly reports that the database is corrupted. See attached screenshot. After reverting to 8.6.2, everything works normally.

This error has also been reported on Reddit.

Another problem is that the message box cannot be closed without affecting the database, so I had to kill the process manually to avoid this. Suggestion: add an [Exit] button that does not modify the database.
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PS..
I also reported this on bugs.launchpad.net/calibre, tho I am not sure it was the right channel.

[Boilerplate4U]

Problem fixed thanks to Kovid Goyal.

Here is the deal with the Corrupted database error. It was caused by an old metax database view of unknown origin.

Calibre 9 removes three long unused columns from the "books" table (isbn, lccn and flags). If something previously created a SQLite view called metax in your metadata.db (likely a third party plugin that somehow needed an extended meta view) then SQLite refuses to drop those columns because metax still references them.

To fix: Click [NO] in the error dialog to avoid creating an empty library, then open your metadata.db with a SQLite tool and run:

DROP VIEW IF EXISTS metax;

Then save, reopen Calibre, and the upgrade should complete normally.