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Remember if you only purchased books from Kobo, synced them from the Kobo store then saving / restoring collection status makes sense.
Now when calibre is configured for automatic metadata management it will update collections on the device to match the defined column(s) in calibre. I'm not sure though what happens if the side loaded book is NOT on the device but the book IS flagged by Kobo as being in a collection. I'll experiment later on
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