Dear Vikram
As per section 77 of cgst & section 19 of IGST, The registered person who has paid IGST on transaction considered by him as inter-state supply, but which subsequently held to Intra-state supply (vice versa) , So wrongly deposited tax can claim as refund, means the wrongly deposited tax is lying in your cash ledger (not being setoff) .
So the above section is specifically speaks of transaction related to Outward supply. hence not applicable in your case & as per section 49 of cgst act the credit ledger balance can be set-off against output tax liability , so you cannot reverse the wrongly claim IGST , need pay in cash ledger & for cgst/sgst credit which was not avail till Sept -19 will be lapsed