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What I did last time I factory reset was in calibre, was tag all books that were on the device in my library with a tag (sort books by on device column), and used the Kobo Utilities to copy reading status and progress from the Kobo into the calibre library.
I then did a factory reset, and uploaded all my books again, let them process, then used Kobo Utilities to update the reading status.
Not perfect, but better than having to start from scratch.
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