Did you find a solution in the end? I've got the exact same problem.
I tried to reconstruct the .kobo directory based off kobo-dir-fresh-1.4.zip in this thread
https://www.mobileread.com/forums/showthread.php?t=88445 but I think those files are too old for the ereader software (v1.9.11).
Currently Kobo Desktop recognizes the ereader but it reports a 'USB error' trying to sync to it.