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I used to have the same problem syncing and I eventually fixed it after manually deleting my collections on the Kobo and my Kobo account (did the latter through the app), syncing, and then reuploading all my collections metadata from Calibre (I also pruned a bit as I was doing that, I had 180 collections and went down to 100). I don't remember exactly what the issue was but I'd found a thread that discussed this and it did work.
Before I did this, syncing through the device took literally forever but I could still sync using the desktop app.
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