To summarise for posterity, and hopefully help someone else out:
1) I began with a functioning Kobo, but very slow synching via the desktop app
2) On Kobo's own instructions, I did a factory reset to address this. I also deleted and reinstalled the latest release of the desktop app.
3) The Kobo attempted to download all my books, choked, and claimed to be full while only containing the first page of each chapter of five books. Sync failed, and for some reason the app did not allow me to choose which books to synch (the plus/minus symbols did not display despite the Kobo being plugged in)
4) After another factory reset, the Kobo tried the same thing. I used Skip to prevent it, then was able to manually select a few books to install.
4a) Both the synched books, and books I tried to sideload, were ignored entirely by the Kobo despite being present on the device. The Kobo thought it was empty.
5) Turning the Kobo off for a while eventually persuaded it to believe in my books. I have not attempted to change it in any way since out of sheer paranoia. Perhaps I will just reread those five books eternally.
From my limited observation, I have no reason to think that the speed of sync has been in any way altered by this alarming two-day process. Nor have I received any response from Kobo to the four emails I sent in reply to their suggestion. Recommendations of more helpful ereader manufacturers will be gratefully received.
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