Well, I have large amounts of egg on my face
I did some more exploration with TreePad and it turns out that there are 2 kinds of tree pad files. by default it stores the nodes as RTF, but if you select the "htlhjt" file kind instead of the "hjt" file kind when you create the project all of the information is stored as HTML in the file.
I also found out what I was doing wrong with the export. If you export the subtree as a series of HTML files the links are not present. If you export the subtree to a "website" then it creates all of the same files (plus a couple of extra ones) but all of the links work fine....
The only wrinkle is that for some reason with the HTML projects you can not include images, but with the RTF ones you can (and you can export the images as part of the HTML export... Do I want to go a little bit further and parse RTF to do my automatic link insertion...
anyway I think I am going to have to get buy a full copy of TreePad. $40 is abuot £25 at the moment so that is not very expensive at all.