Have a question I've not been able to find an answer for, nor come up with my own answer from experimentation.
Let's say www.mydomain.com/index.html has a bunch of inbound links. I make a change in .htaccess to 301 redirect www.mydomain.com/index.html to www.mydomain.com/xyz.cgi/page=index.html so shoppers are automatically issued a shopper ID (SID) upon arrival. Will the SE automatically transfer the value of the inbounds from the old address of www.mydomain.com/index.html to www.mydomain.com/xyz.cgi/page=index.html , or will the new url have to gain it's own inbounds for value?
If you set up a 301 redirect on both /index.html AND your root URL, it will pass on all of the link benefits to the destination page in a short time. However, I would recommend that you consider exploring other methods that would allow you to include the CGI processing into your index.html page without manipulating your site's root URL in the search engines. There's always a way to keep a conventional root URL that incorporates CGI script processing. If nothing else, you can call the script via an <iframe> embedded in your index.html file. Just make sure it ends by generating an appropriate HTML page with something innocuous like the time and date.