You guys should investigate Options > Experts only > Rewrite links.  Probably
"Original/Original".  This keeps the HTML link structure as-is, although the
pages may still be written with .html extensions (I can't quite remember--try
searching).  If you need to serve the HTTrack mirror you should be able to do
some smarts with .htaccess to route the original URLs to their .html
counterparts.

--Leto