I have a Hype project where on each of its 6 scenes there is an HTML5 audio embed. Most browsers, including Chrome will not allow that many embeds on one page. Even though they are different scenes the browser interprets everything as one page.
Matt, I’m not familiar enough with your project to have an informed opinion, however:
What about using the “audio sprite” concept, but instead substituting a Hype Timeline (or possibly a couple Timelines) where your audio resides. This approach might prove easier to manage.
It is very document-dependent, but you may want to use the Advanced Export to export scenes individually. (You’ll need to replace any “jump to scene” with corresponding “Open URL” actions).