An organization's tax-exempt status will be automatically revoked by the IRS if it fails to file IRS Form 990-PF for three consecutive years. In that case, you must either apply for reinstatement of your organization's tax-exempt status or contact the IRS to reinstate your tax status in any one of the four ways provided.
Until the application to reinstate your tax status is pending, you shouldn't file the return as you're no longer exempt from federal income tax and not eligible to receive tax-deductible contributions. Also, your organization will be removed from the cumulative list of tax-exempt organizations by the IRS.
