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I finally decided to copy the books that were only on my reader into calibre, and I may have discovered the cause of the issue. When I plugged in my reader and started to copy the missing books into calibre, I discovered that the books on my reader were in two different folders: The ones also in calibre were in a "books" folder, and the ones only on my reader that I had downloaded wirelessly were in a "downloads" folder. I guess calibre wasn't checking for the other folder, which I'm imagining would possible if I knew how to do it. Anyway, my books on my reader now match the ones I have in calibre, so hopefully I won't have any more missing collections. Thanks for everybody's assistance.
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