As far as I understand it, all Calibre or Desktop app operations are done through the filesystem, copying files to the main storage or editing files in situ, so as long as the drive won't mount on your PC you're hosed.
About Linux, it's fairly easy to run it in a Virtual Machine over VMware player and access the USB port from there. The hard part is finding what to do next... -->
Have you tried contacting the Kobo helpdesk, just in case?