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Originally Posted by Jasmine GreenTea
I am more concerned about the highlights and occasional annotations to EPUBs.
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Export these using Kobo Utilities, except that has to access the database.

You can add a config menu item to export annotations per book on the Kobo, but if the database is damaged it may not work.
There is though currently no way to import other than restoring a backed up database. Except your database is corrupt.
Even if you could re-import annotations, the ebook needs to be same name and identical and in same database record for a separate import of saved annotations to work (which isn't a thing that exists. You can maybe restore bookmarks, reading position and reading status using Kobo Utilities, which can make a backup of that. Not sure why it doesn't also do highlights and annotations. But, again, the database needs to be sufficiently intact.
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As I do have a file-by-file backup of the content of the ereader, would that help? Would it help in case I find that the logout/login erases too much?
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The files have the ebooks, notebooks and settings. Annotations & highlights and bookmarks are in the sqlight database file. The logout & login deletes the database and makes a new one, and any folders/directories created in the Notebook section (and thus their contents, but that can likely be backed up and restored, though I only tried actual notebooks, not folders created via recent FW GUI). Actual ebooks and other notebooks are not deleted at all, but the annotations are in the database file, not the actual ebooks, which makes sense actually.