> WinHTTrack add ".html" to links using folder names before 
> trying to download files from the site.
> for example  <http://thisisatest/folder/1>  
> will become  <http://thisisatest/folder/1.html>

This is perfectly normal for DOWNLOADED links: httrack 
always remaps files according to their type locally, BUT 
the links should not be broken. However, links not 
downloaded should not be touched.

Are you sure this is the case for links NOT downloaded ? 
Can you give an URL or test page please ?