> OK thanks.  I thought the program scanned the HTML
> source and looked for embedded URL paths and not
> actually needed to execute (Javascript) them.

It will replace embedded urls with file references and not execute the
javascript.

But function("path","file") can't be handled.

Your Javascript:glbl_changeURL( '/wps/portal/myhome/HeadquartersLakeCounty')
httrack may try site/wps.../county/ but if that fails what can it do. 
The function could be:
changeURL{ openurl(arg+"global.html"); }
or
changeURL{ openurl("hidden/"+arg+"other.html"); }
or
changeURL{ openurl("/hidden/"+arg+"other.html"); }
etc.
httrack can't try all and then reverse engineer back to the argument to the
function.