This is my sample file
#%cty_id1,#%ccy_id2,#%cty_src,#%cty_cd3,#%cty_nm4,#%cty_reg5,#%cty_natnl6,#%cty_bus7,#%cty_data8
690,ALL2,,AL,ALBALODMNIA,,,,
90,ALL2,,
You could try to delete the empty field in column 4, if column no. 4 is not a two-character field, as follows:
awk 'BEGIN {FS=OFS=","}
{
for (i=1; i<=NF; i++) {
if (!(i==4 && length($4)!=4))
printf "%s%s",$i,(i
Output:
"id","cty_ccy_id","cty_src","cty_nm","cty_region","cty_natnl","cty_bus_load","cty_data_load"
6,"ALL",,"AL","ALBANIA",,,,
9,"ALL",,"AQ","ANTARCTICA",,,
16,"IDR",,"AZ","AZERBAIJAN",,,,
25,"LTL",,"BJ","BENIN",,,,
26,"CVE",,"BL","SAINT BARTH�LEMY",,,,
36,,,"BW","BOTSWANA",,,,
41,"BNS",,"CF","CENTRAL AFRICAN REPUBLIC",,,,
47,"CVE",,"CL","CHILE",,,,
50,"IDR",,"CO","COLOMBIA",,,,
61,"BNS",,"DK","DENMARK",,,,
Note:
length($4)!=4
since we assume two characters in column 4, but we also have to add two extra characters for the double quotes..