IGST paid at the time of import is available as Input Tax Credit (ITC) under Section 16 of the CGST Act. Such ITC can either be utilised for payment of GST on outward supplies or claimed as refund if used in zero-rated supplies.
1. Supply to EOU – Supplies made to EOU are notified as deemed exports [Notification No. 48/2017-CT]. Refund can be claimed either by the supplier or the recipient EOU (subject to prescribed documentation and undertakings).
2. Physical export of goods – Exports are zero-rated supplies under Section 16 of the IGST Act.
You may: Export under LUT/Bond without payment of IGST and claim refund of accumulated ITC, or Export with payment of IGST (using available ITC) and claim refund of IGST paid through shipping bills.
Thus, you are entitled to ITC/refund of IGST paid at import stage, but double benefit is not permissible. You have to carefully choose between deemed export refund route (for supply to EOU) or zero-rated refund route (for direct export).