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Do I need to wait for the file to be converted to EPUB, before I can actually say how the HTML files are split up to single pages, as I can't know beforehand, ( e.g. <a href="./index_split_001.HTML#footnote1 ) or is there a simpler way to circumvent the internal workings of the EPUB file?
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I don't know what could be simpler than to open an html file in Sigil, to link it to a favored style sheet, and then to click on the appropriate icon and merrily split away! That's the way I've handled every ebook since January 2012.
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But once calibre converted the file to EPUB, the links stopped working.
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From all that I have read (and I've read a lot!), you're better off leaving Calibre out of the process if you are serious about publishing, as opposed to managing books for your own enjoyment. To me, Calibre-generated html looks an awful mess. I use it regularly to convert epubs to mobi files so I can read them on my Fire tablet, but I wouldn't dream of inflicting that html on my own books.