I'm having the exact same problem with my Kobo Aura HD. It started right after updating to El Capitan. Even directly after restarting the Kobo I get the "unable to open database file" error message.
I'm having the exact same problem with my Kobo Aura HD. It started right after updating to El Capitan. Even directly after restarting the Kobo I get the "unable to open database file" error message.