Hi JANELLE
You need to first understand how the ATO treats hecs/help debt repayments. Technically there is not such things as a hecs/help repayment via the PAYG Withholding system. Yes an employer is required to withhold extra that 'may' go towards a Hecs/help debt, but it may not. It is not until the tax return is processed by the ATO that a liability for a hecs/help debt arises. If the employee's earnings are below the repayment threshold, all extra tax withheld will be refunded. If not enough tax is withheld, they will receive a bill.
An employee can only make a hecs/help repayment directly to the tax office using a special form/payment method.
If you decided to deduct extra tax instead of simply setting the employee to a Hecs/help tax table, then provided you sent the funds to the ATO with the PAYG withholding payments, the ATO will either refund these amounts if there is no hecs/help repayment due, or will apply the relevant amount against the hecs/help debt.
When funds are sent to the ATO, they are not 'attached' to a particular employee. It is the Income Statement that you provide to the employee (or payment summary) which determines how much of the PAYG Withholding you sent to the ATO goes to each employee. If you have reported the wrong amounts via STP then yes you will need to amend those income statements. So check what you have reported for PAYG for the employee and what you have paid to the ATO.
Fix any mapping in the MYOB file, then lodge an Update event for the employee for the relevant year. MYOB is very limited here and you may have difficulty for FY 2021 and FY 2022. MYOB generally does not give you access to the earlier years to amend. You may need to use restored backups offline, or use other software such as STP Creator to make the corrections.
Regards
Gavin
