This question comes up for me frequently at affiliate forums I moderate and I just don’t have the right answer. I’m always really leery of changing ANY affiliate links at all for fear they won’t track properly – but then again as everyone knows, I’m not all that technical. The concern for merchants comes up when affiliates leap frog the merchant in the SERPs and actually knock the merchant out of the rankings because Google thinks the affiliate IS the merchant. This time the question is a little different because tracking is done through subdomains on the merchant site. Maybe someone wants to go over to Search Engine RoundTable and add their 2 cents to this thread: How To Keep Google From Indexing Affiliate Links & Still Get Credit For Them. PK says

I am having an issue maybe someone with alittle more experience with redirects can help me with…I have to keep track of leads/contacts from referring websites so originallly I created a subdomain for each affiliate. The subdomain would pass along a param to the contact form stating which affiliate the user was on when he/she filled out the contact form. Anyway problem started when Google started indexing all the subdomains as unique websites so some affiliate sites were ranking over mine PLUS by linking to the subdomain my original site was missing out on alot of link juice.

Lee Odden replies with: “Serve Googlebot a non affid url and to 301 redirect any incoming requests that do include the affid to the non affid url. Cookies capture the data to give credit for affiliate sales.” Is that the best way to do it?