It may be that you are looking for something like this:

#!/usr/bin/perl
use strict;
use warnings;
use Text::CSV;

my $file1 = <<FILE1;
number,letter,both
1,a,1a
2,b,2b
3,c,3c
FILE1
my $file2 = <<FILE2;
number,letter,both
1,a,1a
2,,2b
3,c,3c
FILE2

my $csv = Text::CSV->new();
my %masterlist;

open my $f1In, "<", \$file1;
<$f1In>; # Skip header row

while (<$f1In>) {
    if ($csv->parse($_)) {
        my @columns = $csv->fields();

        $masterlist{$columns[0]} = $columns[1];
    } else {
        my $err = $csv->error_input;
        print "Failed to parse line $. in file1: $err";
    }
}
close $f1In;

open my $f2In, "<", \$file2;
<$f2In>; # Skip header row

while (<$f2In>) {
    if ($csv->parse($_)) {
        my @columns = $csv->fields();

        $columns[1] = $masterlist{$columns[0]} if ! length $columns[1]
+;
        print join (',', @columns), "\n";
    } else {
        my $err = $csv->error_input;
        print "Failed to parse line $. in file1: $err";
    }
}
close $f1In;
[download]

Prints:

1,a,1a
2,b,2b
3,c,3c
[download]

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