I did get some advice but I must admit it wasnt an easy fix. The advice I decided to follow was
To reverse the pay run and prepare 2 separate pay runs per the payments made in the bank feed.
So I kept a copy of the payslip then reversed the Payroll
Entered Two payrolls both with the same date processed & paid date
Payroll 1 basically re did the pay but adjusted the Net Pay figures & Adjusted the PAYG TAX to the amount on the original payslip until I got the Net figure that was paid from the bank account then Adjusted the same Super figure
Original Pay slip
4/12/25 to 17/12/2025 Paid 17/12/2025
Gross Pay $2019.30/Net Pay was $1727.30/Tax $292/Super $242.30
Payroll 1
4/12/25 to 17/12/2025 Paid 17/12/2025
Gross Pay $1847.00/Net Pay was $1555.00/Tax $292/Super $242.30
Payroll 2
4/12/25 to 17/12/2025 Paid 17/12/2025
Gross Pay $172.30/Net Pay was $172.30/Tax $0.00/Super $0.00
Then Check YTD figures are all the same as original Payslip
Keep all 3 Payslips together
It is disappointing that MYOB doesn't give the facility to match two payment to a payroll amount
We all make mistakes but it shouldn't be this hard to fix
This is probably not a great way to fix the problem but it did work. I have double checked the figures and they all balance to the original Payroll
Have a great day