Maybe some additional detail will help.

Link A - links to page in the CMS using a relative link, the page actually
exists.
Generated Source in CMS - href="somepage.htm"
As captured by HTTrack -  href="somepage.html"

Link B - links to another page that will exist when the output is copied to
the static host.
Generated Source in CMS - href="someotherpage.htm"
As captured by HTTrack -
href=http://localhost/path_on_host/someotherpage.html

I am entering both links as if they were local relative links. The link that
actually hits something on localhost comes out okay, the other does not.

I was hoping that it would leave the second link intact.