Thanks for your help guys.
The only option I could find is "Preprocess input file to possibly improve structure detection" which, looking at the Calibre User Manual, seems to be the option you're talking about (??).
But this option doesn't fix hyphenation and destroys other elements of the structure (ie. Aboriginal words with individual letters underlined, like Uluru, now have spaces either side of the letter and no underline)
Calibre is also mucking up my cover and title page. Hence the question: can the hyphenation issue be dealt with outside of Calibre?
d.
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