Re-reading that linked thread, I decided to try to force a Nickel scan. Having not the foggiest idea how to do this, I connected my Libra by USB in Nickel, without Calibre running. I then ejected it, scrolled through my entire list of books, and then opened the book I'm currently reading (one of the 3 not showing up in KOReader's Calibre metadata search). Then, I reconnected to my PC, still in Nickel, still without Calibre running. After a few minutes I ejected, fired up KOReader and hey presto! - the missing books are now all showing up.
The reason I'm posting this here is because the earlier thread mentioned chaining USBMS sessions from inside KOReader. In the 5-6 months I've been running KOReader, I've probably run fewer than 10 USBMS sessions in total from inside KOReader before running into this problem, so it was not the cause of my issue, I think.
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