Firstly, thank you all. This board is indeed very helpful.
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Sony readers are not quite the same as other readers. All the metadata for your books (authors, title etc) is stored in a database file on the reader (FYI it's called media.xml). It doesn't much care what filename you gave your books in the Send-to-device template but it does store the filename in the database.
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Very interesting. That could mean that the differences between the reader and calibre over time have their origin in some Sony-buggy-way of messing with this XML and calibre not overwriting it.
Therefore I would be very interested in the following suggestion:
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If you want to make sure that this database always reflects what you currently have in Calibre (without any need to resend to device) then the way forward is a Metadata Plugboard for the Sony. Every time you connect, Calibre updates the Sony database with the latest metadata no matter which book format (epub, pdf, rtf, txt). I don't use Notes and bookmarks much, but as far as I can tell they don't get deleted if you're using a Plugboard.
If you would like some help setting one up I'm volunteering to help. Just let me know.
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Notes and bookmarks are very important to me. Learning spanish and marking the words I don't know and such.