I confirm the issue. This sum of information should be at the Developer Account level. Then, payment methods should be open to modification, addition or removal. App Store specific payment methods should be added by proposing to mirror any of the bank accounts detailed in the Developer Account if any exists (simple users would never see this option), or to create a local one for the App Store specifically. Incidentally, it should then be possible to upgrade (displace) an App Store account to the Developer Account level.

You might want to look into your own software tool. I saw that the one I rely on mysteriously decided to purge all the icons for all the platforms I worked on.