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The only difference in 0.7 is that calibre automatically recognizes books on your device that are also in your library and updates their metadata. Most people would consider that a good thing.
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Well, at first I thought it was because the Sony Reader automatically puts tags and series into separate collections. However, the reader library doesn't do this, only calibre. I think this is why:
http://calibre-ebook.com/user_manual...he-sony-reader - "When you add tags to a book’s metadata, those tags are turned into collections when you upload the book to the SONY reader."
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Assuming you had a version more current then 0.6.17 updating Calibre should not have affected your collections within the calibre library. What version did you update from?
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Whatever the most recent update was, I just updated within the last week.
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Deleting and re-adding them from your reader or from Calibre itself?
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From the reader, as the collections stick around even if they're empty. I figure it's faster to format the device and add books in batches than go through and re-organize each and every book and collection.