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The only other thing I can think of, and this is a long shot, but try running 'sync' in the Kobo desktop application.
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This is a good suggestion. The sync seems to reset the dbase data pretaining to epub files, forcing a reprocess afterwards... might work.
If it doesn't work, copy the database file to your PC and then delete it from the device. Unplug and then reconnect the Kobo. Then do another sync. This will at least eliminate the possibility of a corrupt database.
If you're next step is exchanging the device, might as well go gung-ho first
