Thanks for the advice regarding the books marked as "Download" - I'm perfectly happy reading books loaded straight from Kobo (although I never buy them through the ereader; it's easier to do that on my phone!), so I've bitten the bullet and have gone through over 30 pages worth of books and tapped on the download. I hope Calibre will give me an easy way to spot which copy I can delete!
As for the other issue, erm - I don't know why Calibre didn't update the cached metadata, but it turns out I wasn't using the KoboUtilities correctly - I hadn't realised that I needed to select the books first! D'oh!
Once I selected all books and clicked update, it reported that all but 4 had been updated. A definite PEBCAK issue there, I think! *{;-)
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