Buyers referred to your site via an affiliate hop link will often not actually buy anything from you immediately. When a buyer clicks an affiliate's hop link, we set a referral cookie in their browser that expires in 6 months to ensure that the affiliate, who brought your product/site to the buyer's attention, would still earn a residual commission for their referral if the buyer eventually makes a purchase later, within a time frame when it's reasonable to infer the affiliate's earlier referral contributed to the sale being made.
The default 6-month residual commission period is what we document on our help pages and what existing E-junkie affiliates would expect, so if you choose to shorten that period, you should be clear about that on your site's affiliate recruitment page and paste the URL of that page in your Affiliate Program Settings > More Information URL field, so affiliates can find their way back to that page via the More Info button in their Affiliate Admin.
Adding a custom referral-cookie lifespan to your landing page URL for a given hop link would affect cookies set by clicking that type of link from that moment on, but referral cookies already set by hop link clicks before you'd added the custom lifespan would be unaffected. E.g., if you add a 30 day lifespan to your Common Hop Link landing page URL, all your affiliates' common hop links (including those already issued to affiliates) would start setting a referral cookie that expires only 30 days after the link is clicked, but any product-specific hop links (if you'd set those up) would be unaffected unless you also add a custom lifespan to the landing page URLs for those as well.