An organization will appear to be on the IRS "Auto-Revocation" list if its tax-exempt status has been revoked, most often due to failure to file a 990 tax return for 3 consecutive years. In order to fix this, organizations whose tax-exempt status has been revoked must apply for reinstatement with the IRS via the Form 1024 .
File 990 has resources to assist in the reinstatement process! See: What information does File 990 need to help my organization apply for reinstatement of tax-exempt status?