I am not sure I get whether this is an HTACCES problem or handling requests in index.php proble.
You will need to redirect ALL request that don’t request a file or folder to index.php then break down your request URL in the index file and handle the parameters.
undisclosed.com/welcome/index.php?promo=REFCODE
and
undisclosed.com/welcome/?promo=REFCODE
should work exactly the same way.
In order to remove the ? you need to handle that in your index.php/controller/etc