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Check your settings under
Calibre-Preferences-Sending books to devices-Metadata management
You probably want to set that to "Automatic" (the downside is if you have a lot of books on your Sony it'll take 1-2 minutes each time you connect)
It will then update the tags/collections each time you connect -- the reading list doesn't enter into it at all.
-or-
You can set Metadata management to "Only on send"
Then you'll need to tell the reading list to re-send the books even if they're already on the reader (by customizing the reading list to "Sync all list items to device"), but that will be much slower as it will send the entire book, not just the metadata.
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