Users with Yubikey / WebAuthn / FIDO authentication are tied specifically to the login domain of your site. If you change your site's custom domain settings, every user with this type of 2FA enabled will need to remove their existing 2FA settings and re-configure them. This is baked into the WebAuthn requirement for devices to generate site-specific public/private key pairs, which Files.com follows.

If changing your site settings would impact users, you'll see a message similar to this one when you attempt to change the domain:

"If your site has X users using a Yubikey or Webauthn-based two-factor authentication (2FA) method. These methods are tied to the existing domain. If you change your domain, these 2FA methods will be removed and users will be required to re-register these methods."