In relation to opting out of the Primary Production Averaging there is a twofold process:
Remove Averaging data in Tax Estimate:
You will need to update the taxpayers return properties and remove any averaging data from the Tax Estimate.
Advise the ATO:
It's always a good idea to contact the ATO and let them know as they also retain the averaging data in their servers.
Refer to the ATO for information on opting out of Primary Production averaging.