I suspect you may be able do it by exporting each to different directories as Normal.
And then moving files into just one of them.
Because you are naming them different the hype_generated_script.js should be ok and not overwrite. But any thing with the same name would overwrite.
If the images are the same images then no problem.
There are other hype files though that Maybe a problem if the over write . Like the .htc
I am not sure what that is for so hopefully some one else can answer that.
You would also need to change the path to the resource folder for the html files that did not originally have file in it.
i.e in these two lines
the synd.hyperesources would need to change to the new one.
And any other code line that points to the old folder.
Not able to test this at the mo though..