If the wrong tax Certificate code has been selected for a pay component code in Attache in the setup screen, then you can correct this by selecting the right one.
In the setup screens for Allowances and Deductions, you can select which Tax Certificate Code is correct for the code. The implications on your choice will be reflected when you submit batches to the ATO that include the allowances and deduction. This can affect whether the amounts are included or not included in employee's gross income. Therefore, it is important that you make the correct selection.
Refer to this link on the ATO website about which option to select and when: https://www.ato.gov.au/businesses-and-organisations/hiring-and-paying-your-workers/single-touch-payroll/in-detail/single-touch-payroll-phase-2-employer-reporting-guidelines/reporting-the-amounts-you-have-paid/allowances.
For detailed information on the values in the Tax Certificate Code field in Allowance or Deduction Maintenance, also refer to: Payroll Setups help and user guide specifically referring to the following sections:
The Tax Certificate Code field in Allowance Maintenance section.
The Single Touch Payroll Phase 2 - Allowance Setup section.
The Tax Certificate Code field in Deduction Maintenance section.