Use Text::CSV_XS' csv function with the on_in callback:

$ cat test.pl
use 5.20.0;
use warnings;

use Text::CSV_XS "csv";

csv (in => "test.csv", blank_is_undef => 1, on_in => sub {
    splice @{$_[1]}, 2, 2, $_[1][2] // $_[1][3]; });
$ cat test.csv
1,2,,,5,6
1,2,3,,5,6
1,2,,4,5,6
1,2,3,4,5,6
$ perl test.pl
1,2,,5,6
1,2,3,5,6
1,2,4,5,6
1,2,3,5,6
[download]

update: That also surfaced a small buglet in the code, as I wanted to show that that all fields on output could be forced quoted in the same call, but somewhere that option currently gets lost. The workaround however is easy:

$ cat test.pl
use 5.20.0;
use warnings;

use Text::CSV_XS "csv";

csv (quote_always => 1, in => csv (in => "test.csv", blank_is_undef =>
+ 1,
     on_in => sub { splice @{$_[1]}, 2, 2, $_[1][2] // $_[1][3]; }));
$ perl test.pl
"1","2",,"5","6"
"1","2","3","5","6"
"1","2","4","5","6"
"1","2","3","5","6"
[download]

Working on a fix for 1.18 ...

update 2: fixed. I'll release after going through the long test procedure.

$ perl -MText::CSV_XS=csv -e'csv (in => "test.csv", blank_is_undef => 
+1, quote_always => 1, on_in => sub { splice @{$_[1]}, 2, 2, $_[1][2] 
+// $_[1][3]; });'
"1","2",,"5","6"
"1","2","3","5","6"
"1","2","4","5","6"
"1","2","3","5","6"
[download]