I'm working on an offline website (and hence using the javascript-based version of Zoom Search
My website consists of one main index page...
I assume you are using Javascript with the innerHTML function to load HTML content into the <div>. I haven't tested this but I don't think you can use innerHTML to load an external HTML file, and then have Javascript which is embedded in external HTML execute.
The simple solution would be to have a web site made up of 2 pages rather than 1.
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