OK, but why run that through system when you can just run it directly in perl:

{   my %mons = qw( Jan 1 Feb 2 Mar 3 Apr 4 May 5 Jun 6 Jul 7 Aug 8 Sep
+ 9 Oct 10 Nov 11 Dec 12 );
    my $mon_str = join '|', keys %mons;
    my $mon_re = qr/$mon_str/;

    sub fix_bcp_file {
        my ( $file ) = @_;
        local ( $^I, @ARGV ) = ( '', $file );
        while ( <> ) {
            s/(^|\|)($mon_re)\s{1,2}(\d{1,2})\s(\d{4})\s\s?(\d\d?):(\d
+\d):(\d\d):(\d{3})([AP])M(\||$)/
              $1 .
              sprintf( '%04d-%02d-%02d %02d:%02d:%02d.%03d',
                $4,
                $mons{ $2 },
                $3,
                ( $9 eq 'P' && $5 < 12) ? $5 + 12 : ( $9 eq 'A' && $5 
+== 12 ) ? 0 : $5,
                $6,
                $7,
                $8 ) .
              $10
            /eg;
            print;  # UPDATED thanks runrig
        }
    }
}
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