In exportation the occurrence of a chargeable event is on the day of issue of the invoice, but not later than 7 days from the date of delivery. In your case the occurrence of a chargeable event is in September. If your company has in its possession the document IE 599 before the deadline to submit the VAT return for September the company will be entitled to a 0% rate and indicate that supply in the September VAT return.
If the document was not received by the Company at that date, that supply needs to be indicated in the October VAT return (with a 0% VAT rate) when the company receives the IE 599 document before the deadline for October VAT return. However if, within this period the taxpayer does not receive this confirmation, that supply of goods must be show in the November VAT return as a domestic supply. Obtaining the document IE 599 on the later date will entitle the company to a VAT return correction. In the VAT return for the month the document was received the taxpayer will indicate decrease in the domestic sales, at the same time indicate the exportation with a 0% VAT rate.