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This issue seems to have gone away for me. I posted in this thread about how I could only stop the sync issue by archiving all my kobo books and sideloading them on my Kobo so that my collections only contained side loaded books.
A few months back kobo had an issue where they lost everyone' s archived books, so my entire library was gone. I contacted customer support and they restored my all my books to me. I was afraid to re-archive them until kobo had fixed the problem, so I decided to try downloading them back to my kobo and adding them into collections again (I deleted the side loaded copies first). It has now been a few months since this happened. I've added new downloads to my collections and done several syncs without any issues. It seems deleting books from my account and restoring them was the fix I needed. This would be a pain if you have a lot of kobo books, but you could delete your owned books, find them in the store, and add them back into your account. Kobo will not make you repurchase them.
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