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Originally Posted by aquarialily
Update on this old problem: I figured out the culprit but I don't know how to fix it. I factory reset my Kobo and reloaded and reconfigured everything. The sync was working fine. It only messed up again when I tried to "match" a Kobo downloaded book on Calibre to an entry I had in my library. I had previously downloaded a version from Kobo and stripped the DRM to keep on my HD and had changed some of the metadata slightly (I wanted part of its very long title to be part of a subtitle). I ended up removing the stripped version on my HD from my Kobo and kept the version from Kobo so I could keep annotations but wanted the metadata on my device to match what I had changed so I "matched" the two manually and then updated the cache. It shows a green checkmark now but the result is that my Kobo syncs forever I guess because it doesn't match whatever is in the database? I'm not sure. Has anyone ever encountered this issue and know how to resolve it? Or do I just "undo" it somehow by deleting the whole entry? 
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So, you updated the metadata in the database on the device to match what you have in your calibre library? How did you do that? Manually? Or using the Update Metadata function in my Kobo Utilities plugin?