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Yes, the Sony readers can't do be read when you have the USB cable hooked up, or while they're re-indexing their library afterward. I got a wall charger, which takes care of the charging issue, and since my transfers are infrequent (say, once a week or so) I just let it re-index while I'm in the shower or something.
There is a way to make calibre transfer to the Sony in author_sort order instead of author order. I know there is because I did it. For the life of me I couldn't tell you what it is right now, but someone with a functional clue will no doubt stop by in a few and explain it. It's somewhere in the settings, but calibre has a lot of settings.
Displaying the authors, then all the books by an author, works in calibre; unfortunately, Sony hasn't gotten the idea that we might want to do that, so we're stuck with books in author order over there. One alternative would be setting up collections with author names, but that would make it hard to find one's other collections in a deluge of author names.
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