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It sounds to me like you have a corrupt database. 4.31 was good at sometimes corrupting the database if you side load.
If you use Calibre, use Kobo Utilities to check the database.
If the database is corrupt and you have a recent backup (from Kobo Utilities), copy the database over the existing one.
If you do not have as recent database backup, you can log out and log back in. That will start the database fresh and everything will be removed. Before you do this, copy the contents of the user partition to your computer and you can copy the eBooks back once you've logged back in.
If you use Calibre, you can repopulate the series, collections and other data.
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