A Just-in-Time directory is the directory associated with a third-party identity provider that has Just-in-Time user provisioning enabled. When you delete the directory, all users in the directory are deleted and the Just-in-time configuration is disabled. Because a Just-in-Time identity provider can only have a single directory, when you delete the directory, the identity provider can no longer be used.
To enable Just-in-Time configuration for the identity provider again, you create a new directory.