The error message is the ATO may have actually received the file the first time round. Please check the ATO Portal to see if the Pay Event is there.
If Pay Event is there then normally after a couple of days the Pay Event will update itself to show the Mark As Complete button and you can then just click on that.
Should the Mark as Complete button not populate then, below are the instructions on how to force it to show.
1) Bring up the Pay Event record and click on the EBMS REQUEST link
2) Edit the ebMS Request record and under the Response Info heading change the Status field to "Rescheduled Pull" and Save
3) Go back to the Pay Event record and there should now be a "Mark as Complete" button
4) Click the "Mark as Complete" button and confirm in the popup
5) The Pay Event should now be green and complete