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I'd recommend using the GUI, at least to start. ebook-convert goes with Calibre's default settings regarding chapter detection and page breaks. There are of course arguments for ebook convert, but that can get complex in a hurry. The GUI just takes care of all that for you. You probably just need to remove h2 from the chapter detection xpath and page break insertion settings, but that's dependent on the html structure.
If you want to switch over to the CLI later because you're integrating this with some script, check the debug log and it will show you all the options that were set during conversion - each of those options equates to an argument that can be passed to ebook-convert.
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