Part of this issue has been spoken about on "many" occasions, but I don't recall having seen anything recently regarding this next matter. If I fail to lodge STP, it is true that a subsequent lodgement for the same employee/s will update the year to date figures with STP.
Consequently it has been stated that it is not necessary to lodge that missed STP lodgement. However, today I became aware of some ramifications, if that STP is not lodged, after I located a small pay run which had never been reported to STP. It has to do with pre-fill which is now occurring when one lodges a BAS online.
Above the statement for prefill, details are provided for the W1 figure, which can also be seen with editing the PAYG tax withheld figure. After some investigation after I found a discrepancy with my figure, I discovered that one can click on "You can view details at STP reporting". When one clicks on that, it shows the details for each STP lodgement.
However, the only lodgements that appear are those that have actually been lodged with STP. So whilst STP figures might get updated for any employee included in a missed STP lodgement at a subsequent lodgement, it turns out that quite definitely, the figure for gross payment has not been included in the pre-fill figure, because the ATO only tracks actual lodgements.
I cannot recall now if the same thing happens with the tax figure.
This then will be one reason why a prefill W1 figure can differ to that reported on payroll summary reports. John L G