Yesterday, I casually went through the wiki for
Kobo & Collections, searching for references to pass along to a friend, and I noticed this bit (which I never knew, or if I knew, I forgot)
Quote:
The option also exists to ensure that neither shelves nor their contents (only Kobo format books) EVER sync to the Kobo servers.
To do this, with your Kobo attached to your computer, browse through the directories on it and find the .kobo\Kobo directory. (Note that under Linux and OS/X environments, the .kobo directory will be hidden due to the leading period). Within this directory will be a couple of files; the one you are concerned with is the Kobo eReader.conf file. This file contains various options that are used to control the device.
Open this file in a text editor (on Windows for instance, use Notepad++, NOT Word or Write), and look for a line [ApplicationPreferences]. After this line, add a new line SyncShelves=false. Save the file, and disconnect the Kobo as usual.
The addition of this line will ensure that shelves do NOT get synced to the Kobo Cloud.
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My sync is running correctly so far, but should it go KO again, I'll try this before deleting shelves like I did in the past.
EDIT to add: it seems the option is no longer supported.