If you are seeing two income statements for the same financial year, this means one has been reported through STP in QuickBooks Online and the other has been reported in another payroll software or another QuickBooks file. If you switched files or accounting/payroll software providers during the financial year but have reported STP through both, you will see these two separate statements.
To remove an incorrect statement, you will usually need to reverse or reset the earnings in the software or file that has lodged those earnings. Each software has its own unique IDs and ways of reporting; you cannot use one software to remove another software's STP report. What has been reported in QBO can be amended and re-lodged in QBO, but it will not affect the previous software's lodgements, and attempting to lodge a 'negative' pay event to zero out lodgements from other software is not possible. Example:
John was using Software A to lodge his STP reports to the ATO from July to August 2019 and reported a total of $2000 in wages to his employee, creating 'Income Statement A' which consisted of that month's recorded pay runs.
After moving to QBO in December 2019, he entered in the employee's opening balance of $2000, then continued to record their wages and lodge through STP as normal. At the end of the financial year, he then had 'Income Statement B', consisting of the employee's July/August wages (their opening balance) as well as the subsequent pay runs.
Because John has reported July/August's wages twice in two different softwares, he now has two different income statements. To remove/zero out the incomplete Income Statement A, he will need to access Software A and follow their process to reverse/reset or zero out those earnings. This way, Income Statement B will be the only reported earnings for the year.
Alternatively, he can remove the July/August wages opening balance from QBO and lodge an Update Event. This will not remove the first income statement; however, the total wages reported to the ATO from both statements will now total the correct year-to-date figure as he has not reported the same months twice.
This can get complicated, and the exact steps to follow may change depending on your scenario. We're here to help - feel free to contact our friendly support team if you have further questions.