Refund of waived late fee

I hv filed GSTR 1 & 3B from Jan 2018 to Nov 2018 on 28 Dec 2018.
According to notification issued on 31 dec 2018, late fee has been waived.
While e-filing those returns, I have paid late fee.
Now Do I hv to file RFD-01 ? If yes, then that amount is not shown in cash ledger, so what I do?