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To answer your earlier question, I create "collections" using an old version of Sony's ebook software, as I find this much easier. I have converted books using Calibre and noticed that the tags affect my collections if I don't delete the tags and replace it with the name of the collection which I want it to be in.
Calibre isn't simple to use, but it's worth it when you get used to it (so I've been told!).
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