As of July 10, 2020, the behavior of the Billing Portal has changed for sites with the Multi-Gateway feature enabled.
During updates via Billing Portal, the cards are directed to the gateway set up as a default gateway for credit cards.
For example, if a customer has a credit card that is stored in Stripe, and then Braintree is added to the site and made the default gateway for credit cards, then when that customer updates their card, it will be stored in Braintree instead.
Previously, updates were directed to the same same gateway where the payment information was vaulted.