Good news, yes you can. I've recently built a tour of a private school in html5 with multiple maps.
You need to place the map viewer into a popup window for html5 to show it.
My multiple maps run off the thumbnail but I think you could initiate separate maps using a control button.
One problem I did encounter was the maps when published in html5 had background markings that weren't originally present. I was using png files that were transparent, that might have been the reason.
To overcome that problem is simply replaced the maps of the published html5 tour with the published flash tour maps.