Because the lodgement being made is after the Payroll Payment Date , you won't be able to submit a "Normal" event anymore.
The only option will be to do an "Update" event. This is something decided by the ATO in their STP Reporting guidelines. Additionally, in Microkeeper we do still continue to send through the Year to Date totals for the financial year, the ATO just will not display the Gross or PAYG totals to pre-fill your BAS when you submit an Update event.
Best practice for STP Lodgment is to ensure that you always report STP on the day payroll is processed as your final step.
That all said, this restriction won't have any affect on the totals to be reported for EOFY, as the Payment Summary amounts are only based upon the Submission that you mark as "Final", which is done when finalizing your final payment for the financial year.