> The customer logs in to the billing interface ( which remains active for allowing users to update their CC in case of problems), he adds in his CC again AND p

> The customer logs in to the billing interface ( which remains active for allowing users to update their CC in case of problems), he adds in his CC again AND pays the last invoice again. Then the next day he does a second chargeback. Sounds like in case of chargeback, you should lock out customer account until they contact support. If this was an honest mistake - then unlock is one email away. If it's not, you are not messing up your chargeback rate.