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Does the latest version of the Kobo desktop for linux not offer to update the device when syncing? I installed the Kobo software on my Windows 7 work machine to perform the upgrade and since use it only with the Kobo desktop on Ubuntu 10.04.
I suspect the reason why the USB update is the only official end-user authorized method is done for support reasons, it seems to work for most people and it is easier to a single update method than provide several different methods for computer-illiterate users, novice PC users and power users. Since Kobo's support people are going to the extra effort of mailing SD cards to people or having Kobo units shipped in that the effort involved in formatting and transferring the update to the SD card is not insignificant.
If you're using Linux and don't have access to a Windows machine then I think the easiest solution is to simply go into a Chapters/Indigo and have the update done there (assuming the Kobo desktop app doesn't perform the update). Also if there is a problem with the update they may be able to do more to help you.
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