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.
I’d be curious as to the intent of “fixing” internal links and what that really means. My expectation would be that formerly: /mydirectory/page.html import as: /mydirectory/page/ and a previous link to page.html at /mydirectory/ would now be to /mydirectory/page/. However, when I go to /mydirectory/ in WP all the links are still referencing .html files as in the previous site. Essentially, zero fixing occurred. Each link has to be gone through one by one and set to the new permalink structure.