My understanding is that the tags are held in a database in the main memory... I'd imagine the Sony software can't distinguish between cards. So when the database info doesn't match the files on the card (which they won't when you replace the card) it's going to clean the database of the "old" info and replace it with the "new" info from the files on the currently installed card.
Calibre keeps the tags in it's own database on your PC, and updates the device's database as part of the process of copying the book files over.
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