LUT not applied

No , as it's clearly prescribed in Rule 96A the LUT need to furnish before export without payment of tax .
It's better pay in cash & file DRC 03.


Note : Sez is not required pay the IGST amount charged by Supplier in his bill when it's procure for authorised operations by him.Its supplier who need to apply for refund under rule 89 of CGST Act.

So it's better you pay in cash and file DRC 03 or declare it in GSTR 3B as the case may be.

After payment whether I can get refund. As simple procedural lapse i loose benefit.