It is good to know you were able to check with the ATO that the pay run lodgement was received. If the pay run lodgement still showed error in QuickBooks Online Payroll, I would recommend contacting our Customer Care Team. That way, they can request the pay run lodgement status to be change to Successful in QuickBooks.
Here's how to contact customer support:
Click on the Help (?) icon.
Select Assistant and enter Contact support in the chat field, and then click the Send icon.
You'll be asked about your concern, and you'll need to enter and send it.
If you can't see any related topics to your issue on what they shared, select No, get me a human.