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Normally one would add to Calibre the file that would be the top of the tree in a browser, and that would pull in the remaining files. Calibre puts all the files into a ZIP file. As you were getting conversion errors it might be worth looking inside the ZIP file to see what has actually been added - maybe you need to add some more files manually?
It is also worth checking what the expanded file looks like in a browser. Many of the "expanders" do not seem to leave you with content that is formatted usefully. Conversion by Calibre is not going to magically tidy up any formatting issues.
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