2 payment summaries sent to ATO

I sent a payment summary to my STP and then realised that I had not sent my June payslips, so I sent June payslips and then resent payment summary. I thought that the second one would override/amend first one but this was not the case. Now my employees have 2 payment summaries in their MyGov accounts one “tax ready” the other “not tax ready”. Why did system not amend. ATO advises me that they will manually override it but is there a way to fix it on my end?