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mrspaceman -- Kolenka is a user here and he is the primary developer of the T1 calibre plugin.
To my understanding of following his work when he created the plugin -- he essentially reverse engineered the process of how Sony handles metadata updates (including some the strange behavoir) so if you use Calibre to manage your ebooks, it will not interfere with any other way of using your T1. So if you use Sony's SQLite db's for to get your metadata it will work for calibre users, drag and drop (and also assuming Sony Reader software).
Maybe Kolenka will check in here and elaborate if not maybe you can PM him to look at this thread he can hopefully help since he probably has the best understanding of how the T1 manages the books metadata.
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