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Thanks for your post. If you wanted to adjust the pay transactions you'd need to lodge an amendment with the ATO as you'd need to adjust the gross wages to reduce the net amount. Your other options would be to pay the employees the short paid amount, you wouldn't need to adjust the pay transactions as the net amount of the pays is correct. Or, write off the short paid amount.
I'd recommend checking with the accountant and employer to make sure payroll obligations are met.
Once you know how this is going to be handled I'll be happy to assist with recording transactions in the software.
Please let me know how you go.
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