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Thanks for the suggestion eschwartz. I just did a quick test.
My test author was Banana Yoshimoto (吉本 ばなな) who is filed as [Ji Ben banana]. I tried just adding an s, closing the metadata screen to save the change, and then removing it. Unfortunately, even though my import preferences are now set to "do not transliterate", this simply renamed the folder to [Ji Ben bananas], then returned the contents to the original folder when the s was removed.
I then tried giving her a different name entirely, and then restoring her name. This had the same effect.
Finally I tried a weird hack to test this: I changed her name to Yoshimoto Banana (not currently a folder name used by any other book) [吉本 banana]. This put the book in [Yoshimoto Banana]. When I switched to the half-kanji half-romaji name, Calibre nevertheless decided this was equivalent to [Ji Ben banana] and put it back in the original folder.
So my observations:
* setting transliteration preferences has no effect when changing metadata of existing books, presumably because they work a different way? Or is this behaviour built in? What happens if you import a book with transliteration preferences set to retain original characters, then change the metadata - will it suddenly romanize it? I didn't test that because it's past midnight, and also (as noted) I don't want anything weird happening to my books because I can't restore them.
* romanization is liable to conflate authors who are actually different people. No idea how likely it is to actually happen, or whether this would present a problem for normal operation of Calibre.
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