Sorry, didn't see your extra questions before I posted.
Have you checked this part of my instructions?
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Just a caveat here... if you're using a metadata plugboard to remap the Sony's Author field then you should make sure that Prefs - Plugins - Device Interface - Sony (or SONY PRST1) - Customize - Use author sort for author is UNCHECKED. Otherwise your plugboard info will be overwritten by the simple author_sort field.
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The PRST1 doesn't have a 'mark as read' function that I know of. There is a special Collection called 'Unread Books' which lists all the books you haven't opened yet. Personally I delete books from the reader as soon as I've read them and mark them as 'Read' in the calibre library.
Another option, suppose you are using Tags to define your Collections then if you add a 'Read' tag (in calibre) when you finish the book, the book would automatically appear in the 'Read' Collection on your PRST1 next time you connect.