Once you delete an affiliate from your program (in Seller Admin > View/Edit Affiliates), that should prevent them from earning any further commissions and ban them from rejoining your program, although it does not revoke any commissions already earned before you'd deleted them, so you'd want to check your monthly masspay commission report and delete the line for their pay-out before you upload that file to PayPal.
Affiliates can change the email settings for their account at any time, although their E-junkie ID number would always remain the same; also, the PayPal Email where they receive payments may differ from the affiliate's Login Email identified in your Transaction Log (both are shown in your View/Edit Affiliates screen). The affiliate referral cookie format can seem misleading; the cookie is named ej_aff_idXXXXXX (where XXXXXX is the merchant's E-junkie ID, not the affiliate's), and the affiliate's E-junkie ID would then be set as the value/content of that cookie.
If you want us to investigate further, please provide us with more specific details, such as the affiliate ID and emails, any page(s) where the affiliate's link was placed, and any affected Transaction IDs? Feel free to email that to us if you'd rather keep it confidential: