An update on this was resolved:
Phoned MYOB and they advised I should process the pay run as it originally went through, send the report to the ATO, then once that new pay run had been accepted by the ATO, send an 'Updated Event' from MYOB's browser STP payroll centre.
I did this but when I went to submit the report to the ATO after processing the pay run, MYOB had two options on how to submit the pay run - as an updated pay run or as a new pay run. I submitted it as an updated pay run to the ATO and after checking both our MYOB and ATO accounts online, it all appears to tally up as it should do.
