You'll want to apply this function to $line before you split it into @fields.

while(...)
  chomp($line);
  $line = join '', grep { $i++ % 2 ? {s/,/ /g} : 1} split /"/,$line;
  @fields = split(/,/,$line);
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Does not seem to be working. I am using a test file with only five lines in it for now (the actual file will have millions of records). Here is the error I'm getting using your line -

Use of uninitialized value in join or string at AlterDataNew.pl line 2
+9, <$FH> line 5.
Use of uninitialized value in join or string at AlterDataNew.pl line 2
+9, <$FH> line 5.
Use of uninitialized value in join or string at AlterDataNew.pl line 2
+9, <$FH> line 5.
Use of uninitialized value in join or string at AlterDataNew.pl line 2
+9, <$FH> line 5.
Use of uninitialized value in join or string at AlterDataNew.pl line 2
+9, <$FH> line 5.
Use of uninitialized value in join or string at AlterDataNew.pl line 2
+9, <$FH> line 5.
Error parsing time at /usr/perl5/5.12/lib/sun4-solaris-64int/Time/Piec
+e.pm line 470, <$FH> line 5.
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And here is the entirety of my script currently with your line added -

#!/usr/bin/perl/

use strict;
use warnings;
use Data::Dumper;
use Time::Piece;

my $filename = 'tested.csv';

open my $FH, $filename
  or die "Could not read from $filename <$!>, program halting.";

# Read the header line.
chomp(my $line = <$FH>);
my $i = 0;
$line = join '', grep { $i++ % 2 ? {s/,/ /g} : 1} split /"/,$line;
my @fields = split(/,/, $line);
print Dumper(@fields), $/;

my @data;
# Read the lines one by one.
while($line = <$FH>) {

# split the fields, concatenate the first three fields,
# and add it to the beginning of each line in the file
    chomp($line);
    my @fields = split(/,/, $line);
    unshift @fields, join '_', @fields[0..2];
    $_ = join '-', (split /\//)[2,0,1] for @fields[14,20,23];
    $_ = Time::Piece->strptime($_,'%m/%d/%Y %H:%M')->strftime('%Y-%m-%
+d %H:%M') for @fields[38,39];
    push @data, \@fields;
}
close $FH;
print "Unsorted:\n", Dumper(@data); #, $/;

@data = sort {
    $a->[0] cmp $b->[0] ||
    $a->[20] cmp $b->[20] ||
    $a->[23] cmp $b->[23] ||
    $a->[26] cmp $b-> [26]
} @data;

open my $OFH, '>', '/swpkg/shared/batch_processing/mistints/parsedMist
+ints.csv';
print $OFH join(',', @$_), $/ for @data;
close $OFH;

exit;
[download]