One popular trick (generally speaking as a Web dev) is to append a unique ID to the .js files referenced in the HTML. Actually, it would be convenient if AppGameKit did this automatically with a timestamp of the current build time, to avoid the caching issues including by users who may be viewing the app using older data.
script.src = "AGKPlayer.asm.js?v=20171208120005";
If you rename the HTML file to .php and your server supports PHP, you can also add this to the very top of it to force disable cache from the server.
<?php
header("Expires: Tue, 01 Jan 2000 00:00:00 GMT");
header("Last-Modified: " . gmdate("D, d M Y H:i:s") . " GMT");
header("Cache-Control: no-store, no-cache, must-revalidate, max-age=0");
header("Cache-Control: post-check=0, pre-check=0", false);
header("Pragma: no-cache");
?>