Hi CollTspt,
I can see why you’d want to update the BAS now that the late invoice has come through. If the BAS has already been lodged, deleting a draft won’t undo that lodgment. Depending on the type of error and ATO rules, you may be able to correct it on a later BAS or revise the lodged statement. Check the lodged statement in ATO online services for a Revise option, or confirm with your tax or BAS agent which option applies.
The ATO explains the options here: Fixing BAS mistakes or making adjustments and Revising an earlier business activity statement.
I hope this helps!
Regards,
Earl