Thanks for all the messages.
I will try to manually install the latest update - just to confirm, it doesn't matter that my device hasn't registered it automatically yet? I don't want to mess up the device further by installing an incorrect update.
If that doesn't help, I'll try a factory reset - I'm sad to hear I won't be able to save my information / account settings, but it's more important to me to have the device back up and running. I hope kobo somehow manages to implement a user settings back up/restore option someday.
I understand that it wasn't the firmware upgrade that scrambled the device, however it seems to have been a trigger for the corruption to either occur or for a previous corruption to reveal itself. I didn't mean to suggest that Kobo is releasing corrupting firmware, rather it was during the timing of updating that my device seems to have become corrupted.
I hadn't updated my kobo for a long time, due to having changed wifi settings a long time ago and neglecting to update the e-reader settings. Perhaps the update was just too big a change and exposed the corruption.
@davidfor - I get the normal "error communicating with device" in Calibre, however once choosing OK, the device shows up as connected, though with apparently no books on the device.
@DNSB - I think that could be the case - I hadn't done a full restart for a long time, so it may have been the restart, not the update that triggered the corruption.
Thanks again for all the tips, you guys are really helpful