I ran into something like this. My card had just expired and been replaced. The card number did not change, but the expiration date did as did the 3-digit code. I wanted to make sure supercharging would work and didn't want to rely on Tesla being one of the businesses that automatically updates card info. I went into my account (web browser, not app), tried to update the card, couldn't find a way to edit the card (new date, 3-digit code), couldn't delete it because there must be at least one card, and then noticed Apple Pay was there. So, I made that the default since I had just updated Apple Pay.
While driving a few days ago, I charged, and then received a warning on the M3 display saying that payment had failed and no more supercharging was permitted. I went online again, found the unpaid charge, paid it, and then looked at payment methods and saw that Apple Pay was default. I switched to my credit card as the default and deleted Apple Pay.
Everything seems to work. I did end up calling Tesla to make sure that things were good on their end because I was at a highway rest stop about to drive a leg that would leave me at about 10% SOC in cold weather and really, really, needed to know I could recharge when I got there.
I'm afraid this note is mostly noise except to say, yeah, it can be confusing. Tesla was helpful on the phone and that may be your easiest path if you want to confirm all is well. That all being said, my bet is that if I had done nothing at all, it would have auto-updated the card info and Just Worked.