This may help you
Input
$ cat f
id,c1,c2,c3,c4,c5...
1,0,acc,123.4E+03,0,bdd,...
2,1.299E-05,bef,1.666E-08,23,ghh....
Output
$ awk 'BEGIN{CONVFMT="%.9f"; FS=OFS=","}{for(i=1; i<=NF; i++)if($i~/^[0-9]+([eE][+-][0-9]+)?/)$i+=0;}1' f
id,c1,c2,c3,c4,c5...
1,0,acc,123400,0,bdd,...
2,0.000012990,bef,0.000000017,23,ghh....
From man awk:
A numeric expression is converted to string by replacing expr with sprintf(CONVFMT, expr), unless expr can be represented on the host machine as an exact integer then it is converted to sprintf("%d", expr). Sprintf() is an AWK built-in that duplicates the functionality of sprintf(3), and CONVFMT is a built-in variable used for internal conversion from number to string and initialized to "%.6g". Explicit type conversions can be forced, expr "" is string and expr+0 is numeric.
So you can arrange CONVFMT variable on the beginning or format field.
