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Regarding the original question, I use Calibre for 98% of everything I do with my Sony. I use the Sony software to buy (rarely) or download free (slightly less rarely) books from the Sony store. I also use it to import notes, once in a long while. Anything to do with loading the books or making collections, I use Calibre. Even the books I buy from Sony, I save in Calibre and load from there.
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