The HTML files are exported from HYPE so you can export many HTML versions from one document. If you export to the same folder it will ask you to replace a previous export if one has already been made. You mentioned that you have put the HTML file through some form of "Translation" so I suggested exporting to a different folder to retain that "changed" HTML file. You cannot "link" them as the HTML file is an export from the Hype document. You change things in the HYPE document and then re-export. All work is done in the HYPE document.
The generated script contains all the changes that you've made in the HYPE document.
It's this file that is called in the HTML file that gets exported.