Builders - advances - gst - subsequent billing

Sir,

In builders cases, we are collecting the advances and accordingly GST is discharged on advances and getting reflected in the R1 Return in the advances tab. But by the time it is billed it may be more than 2 years or three years based on size of the construction but, advances shown in the R1 return can be amended only till to the September Return of the subsequent year. So, in this case, when bill is billed after two years or three years, how to amend the invoices from Advance to invoice. Kindly advise.