I have come up against the same issue now that I am publishing in HTML5, as previously all of the htm and swf files were able to be in the one folder. I have 8 modules in my learning package and I need to be able to go from Module 1 to 2 and for HTML5 each is in its own folder structure. As you are aware the normal relative path of ../Module2/index.html won't work. I have got around this by putting a small html file in Module 1 that only has a meta tag in the head. I set content=0, so there is no delay (0 seconds), it just opens the url. Eg
<html>
<head>
<meta http-equiv="Refresh" content="0; url=../Module2/index.html">
</head>
<body>
</body>
</html>
Even though it is a bit of a pain to have to do it in each module, I am happy with this workaround.