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Originally Posted by Cootey
Both excellent questions. I don't have an answer for you. I'll look into it. Where would I find collection management settings in Calibre just in case I've accidentally turned something on?
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Look up one post. I answered this while you were writing this post.
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As for your second question, these are purchased or borrowed kepubs. I wasn't surprised that sideloaded books needed to be reorganized. (But I'm always pleasantly surprised that they survive a reset.)
I only have one sideloaded ebook on my iPad that differs with the dozen or so on my KA1 LE. They aren't the issue. It's definitely a cloud sync issue—unless I've configured Calibre to do something I didn't intend. With your help, we can rule it out. Thanks for both of your replies.
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No matter what the settings are, the collection management that calibre does should only affect books that are on the device that match with books in the library. If it isn't doing anything, then it is going to be some interaction across Kobo's servers. Are the clocks set correctly on both devices? The syncing uses timestamps, so if the clocks are wrong, the device with the latest time will probably win.