When users access an organization with SAML SSO, GitHub stores a link between the SAML identity and the user's GitHub account. This link is used by SCIM and team synchronization to grant access within your organization or enterprise. If you break this link by signing into that organization with a different SAML identity, you are likely to lose access to resources inside that organization.
Starting gradually today and being fully rolled out tomorrow, users will see a warning message if they attempt to sign in with a different SAML account and change their linked identity. They'll have the option to go back to their IdP to sign in with a different account, which is usually the correct option. If they really intend to break the link to their previous SAML account and link to a new one, they can choose to continue.
Learn more by reading "About Authentication with SAML SSO".