If you had paid tax through e cash ledger than you need to apply for refund and need to pay IGST first, in case you made payment through e credit ledger than not an issue, you can show IGST tax, and reduce your CGST and SGST liability in the subsequent month GSTR 3B. for refund you can go to refund tab and make application and select reason for payment of tax CGST and SGST instead of IGST and vice versa.
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