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Yes, this happened to me several times on my Aura HD. Synching sometimes destroyed my collections, but only the books I added via the Kobo desktop. The sideloaded-via-Calibre books always remained in their collections. Eventually, I gave up on the Kobo desktop and now I only use Calibre to create collections. Maybe consider using Calibre. I was reluctant at first, as it just seemed too big and complicated, but then I just sat down one day, read a few manuals on using Calibre, and I'm glad I did.
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