GoAffPro provides you with the option for affiliate conflict resolution.
To resolve affiliate conflict, go to the Advanced section in the Settings tab of the GoAffPro admin panel.
Here, go to the Affiliate Conflict Resolution section.
Now, select the affiliate who you want to credit for the referral sale if the customer comes to the store using two different affiliate links.
In the case of "The first affiliate" option, the first affiliate who's referral link was used by the customer to visit the store will be credited with the sale.