[scoobertron]

nope, I just unzip the files in the .kobo directory and then unmount it. I have done a couple of resets, but that is only when I feel like going back to the original firmware, and I haven't noticed any difference if I upgrade from a freshly reset device.

Unless my experience is unique, it might suggest that the issue is not so much the upgrade as re-syncing the database with regard to kobo content. I may just have been lucky though. As I mentioned, I only use sideloaded epubs, and have reading life etc turned off, so I have nothing to sync with kobo (which is why I wondered if I might be an interesting data point).

With regard to the steps listed above, I wonder if it might be better to do the manual firmware upgrade before syncing the device, so you are doing the upgrade on effectively a bare device, and then sync up the content on the new firmware. After all, I don't think the device needs to be logged in to copy the files over.