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If there is only one HTML file in the Zip file created by calibre then it means that the other HTML files were not referenced by that one.
If the HTML file you added had included links to all the remaining files then calibre would have pulled them in as well, and treated the whole set as a single book. That is the reason HTML files end up as a zip - an HTML based book consists of multiple files and calibre needs to store each book format as a single file.
It sounds as if in you case you would need to manually creat an HTML file that was simply a list of links to the other files in the right order (in effect a table of contents) and then add this HTML file to Calibre.
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