I’ve just released version 2.1 of HTML Import, which includes a new option to fix internal links. As the importer runs, it builds a list of old paths vs. new permalinks. You’ll see that list reflected in the
.htaccess redirects when the import is complete. This new function runs after all the files have been imported, so it can use that list to match up link URLs with the new WordPress posts.
Like the image import function added in 2.0, the link function should be able to handle relative links:
<a href="http://foo.com">foo.com</a> <a href="/images/foo.png">foo.png</a> <a href="../../foo.html">foo.html</a>
The new option is a checkbox in the Content section. Give it a whirl, and let me know how it goes in the support forum.