> 1> Is there any function used by Httrack which changes 
> the '=','&' signs into '%3D' and '%26'?
Yes - they might be escaped as "unwise" characters (as per 
RFC2616), I'll check that - but the result should be 
exactly the same!

> 2> I think when httrack downloads the files it takes the 
> naming convention used by the browser. Can you please 
tell 
> me in which function these are taken care of?
The htsname.c routines (url_savename() routine) is handling 
the naming conversion ; the parser unescaped before that 
what was unnecessary to escape (for example, %41 as 'A' 
character)
You may also look at htsparse.c, there are two blocks:
if (!no_esc_utf)
  escape_uri(tempo);     // escape with %xx
else
  escape_uri_utf(tempo);     // escape with %xx

which escape the final URL written (I assume this is what 
you want to change)