If you missed the tax exemption filing window for the year of assessment, you are NOT allowed to file for tax exemption in the following year of filing window.
You must appeal to LHDN through a process known as “rayuan khilaf” within 5 years from the year of tax filing, subject to LHDN terms & conditions and processes.
This FAQ is taken directly from the SC's FAQ on ECF Tax Exemption.
For more details on how to make an appeal to LHDN, please refer to the process on LHDN's website.