Slowness with KEpub and disappearing highlights sounds like a corrupt (or otherwise non-working) database to me. You might just need to reboot/restart the device. If that doens't solve it, you might have to use the "log Off" option. That will erase your database, (you will loose all saved pages, bookmarks and highlights,) and require to re-register the kobo before you can conitnue using it, but should solve any database issues.
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