Show Correctly into GSTR-9C, as 9C is also certified by a CA and then you might submit a rectification request to department that GSTR-9 was erroneously filed Nil.
If any one made mistake in gstr 9 then my opinion file 9c (not matter applicable or not) ... 9c is the compare of your gstr 9 and books of account . if you make mistake in gstr 9 you can see in gstr 9c and you fill the suitable reason for it and Dsc signed by CA