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I am setting up an affiliate program through e-junkie.

My question is, suppose my affiliate starts marketing with the link, and the prospective customer clicks on the link and then enters their email address into my database. But they don't make the purchase right away.

In fact, it may take several more emails.

When that prospect returns, will e-junkie recognize that customer and credit it to the affiliate?

Or do I have to capture the affiliate code in my email capture form and re-insert that whenever I put a link to the website's sales page?

Thanks.

Yes, E-junkie's affiliate hop-links set a cookie in the buyer's browser that expires in 6 months, so it's not necessary for the buyer to purchase immediately after clicking the affiliate link in order to grant commission on that sale. You may be interested in this discussion which goes into more detail about how our affiliate system and the various link types actually work:
http://www.e-junkie.com/bb/topic/2690