Are you using adb? I've managed to run adb from a Linux distro over USB. I've found some promising adb commands on this page
Especially the "adb recovery" - it may very well be functional on Kobo. Just be aware the that recovery*.zip file in mmcblk0p2 contains older binaries (September 23), whereas the current binaries on my Vox are of October 27 (presumably the update when I used Kobo for the first time). I think it still should be okay, to revert to older binaries, as then the Kobo's "update" process should do the upgrade.