>Is there a way to make HTTrack ignore the parameters 
and 
> make each message just point to index.html (without 
> any parameters) so that the multiple copies aren't 
> necessary?
No, this would require a specific option - because 
there isn't any way to "know" if a parameter is used 
or not in an URI - except by downloading it and check 
is the content is identical to a content that has 
already been downloaded.

But why is the index.html used with a supplemental 
query string? If this is a trick to avoid caching, it 
would be much wiser to use somehing like md5 content 
id, or even better some "no cache" pragmas in HTTP 
headers.