> For example
> <a 'rel=nofollow' href=http://www.example.net/ 
> ****converts as expected
> 
> <a 'rel=nofollow' href=http://example.net/
> *****does not convert to an relative link - stays
> absolute

This is not a conversion issue, but httrack won't download anything outside
the default mirror scope unless you change the settings.

Just go in Options / Scan Rules, and add:
+example.net/*