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A bit strange, Jon. I just sent 11 ebooks to my device that were singletons so 11 different authors. After the files were imported, I checked that I could open them. I then reconnected to calibre and deleted the files from calibre's remove matching books from device and oddly, the empty directories were also deleted. I did not test this by deleting books from the Kobo GUI since your statement above seems to say that using calibre to delete the last book in a directory does not also remove the directory.
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