Hello Mathilda
Great to hear the pay in question has now gone through STP. I may have misread your initial post though, as I thought you had entered those five weeks into MYOB with intent to have them pulled into STP reporting.
Ultimately whether you leave them in Quickbooks or not is up to you, it's just important to note whether or not they were reported through STP with Quickbooks. If they were done through STP in Quickbooks and you leave them there and do not enter them in MYOB, there should be no issues as the ATO "will have the first 5 weeks from Quickbooks and the last week from MYOB." That would be correct.
But if you would prefer to have everything in one place and process those 5 pays through MYOB STP, you would just want to ensure the pays in Quickbooks are voided according to the ATO. That way when the ATO looks at the BMSIDs for this company, they don't take into account five weeks of pay reported under two BMSIDs. I suppose it's just a preference of bookkeping but as I understand it, the key is just to make sure the data is not duplicated.