Understanding the difference between customer portal payments and
It is important to understand that the customer portal payment method that is saved is not the same as the one used for pre-approval.
The customer portal details are used for customer initiated purposes only ie. payments made from within the customer portal. Customers can schedule autopayments from there, but it is not the same as you having authority to automatically debit them as you do with a pre-approval.
Pre-approval payments such as those that are scheduled to automatically occur as a result of invoices from a connected accounting system, will only come from the stored payment method on the pre-approval form. You can update these details by going to your customer's details screen and clicking Launch Pre-Approval Page, or send them an invitation to update the pre-approval form by clicking Send Update Pre-Approval Email.