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In Citra, you can install the update by going to File > Install CIA and selecting the decrypted .cia file.
Are you having trouble this specific update on an emulator, or
Applying the update typically does not delete your save data, but it is always recommended to back up your .sav files first. ⚠️ A Note on Security
Resolved an issue where players were unable to access the Elder Hall in certain conditions.