You could set up via wifi and avoid the desktop altogether, then there would be no problems. The Kobo desktop application is entirely optional, you don't need it to charge the reader, load books, upgrade firmware, or anything else that I can think of. The only time it is really needed is if you don't have wifi.
(I have never used the Kobo desktop, so maybe someone else will know of a use for it that I can't think of).
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