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It is normal for Calibre to add an HTML file as a ZIP. It does this because most HTML based ebooks consist of multiple files and Calibre can only store one file for each format.
Epub fils are also ZIP files under the covers. However they normally contain additional files that are not in a standard HTML book. i think that the rename worked for you is just dumb luck - perhaps the HTML file you added was actually part of an unpacked EPUB book?
Quite why your original conversion failed is difficult to determine without looking at the actual files input to the conversion.
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