The "Remove a repository from an app installation" API has been updated to fail early if attempting to remove a repository from an application that is installed on all repositories.

To switch an application InstallationState from the all to some state in your organization, an organization owner or application manager must make this change within the UI, while picking up to 50 repositories for the app to continue to have access to. From there, additional repositories can be added via the UI or the "Add a repository to an app installation" API.

To learn more about managing application installations, see "Modifying repository access". For details on the GitHub App REST API, see "GitHub Apps".