Fixed
By deleting the following files:
/Users/<username>/Library/Preferences.com.kobo.Kobo Desktop Edition.plist
/Users/<username>/Library/Saved Application state/com.kobo.desktop.Kobo.savedState
..and folder
/Users/<username>/Library/Application Support/Kobo/Kobo Desktop Edition
..and reinstalled the app, it triggered the new account login in the app and synched just fine.
Toadsfather
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