How did that book get onto your device in the first place? Was it from Kobo? If it wasn't I can't understand why it would come back after the factory resets. Does it show in the library list as a "KOBO EPUB" or something else? What happens when you try to delete it on the device?
I don't know what is causing this, but I know what I would do. I would be looking through the database on the device to examine the record for the book and try and work out what was wrong. After that, I'd either delete the record, or change it to make disappear. The latter would be so that a sync with Kobo wouldn't bring it back. But, if you don't have SQL knowledge, this isn't practical.
If the above didn't work (or for someone who doesn't know how to) I would suggest uninstalling and reinstalling the Kobo desktop app. I would also make sure to removed all traces of it (there is a database and copies of the books), and download the latest version. After the install, do a factory reset of the device and then set it up again. If the book comes back after that, it is a problem on the Kobo server and you should complain to them.
When I have had blank pages when reading the epubs, it has always been a font problem. Changing the size or font usually fixed this.