Working, tested code:

use strict;
use warnings;

my $usage_message = "usage: $0 input_file output_file\n";
die $usage_message if @ARGV != 2;

my ( $input_file, $output_file ) = @ARGV;

open my $in_fh,  '<', $input_file
  or die "Could not open input file 1 '$input_file': $!";
open my $out_fh, '>', $output_file 
  or die "Could not open output file '$output_file': $!";

while ( my $line = <$in_fh> ) {
    chomp $line;
    
    warn unless length($line) == 210;
    
    if ( $line =~ m/^2/ ) {
        # Do Nothing!
        # A line starting with a '2' is a
        # header and is left unchanged.
    }
    else {
        # Change postions 100 and 149
        substr( $line, 100-1, 1, '9' );
        substr( $line, 149-1, 1, 'Z' );
    }

    print {$out_fh} $line, "\n";
}

close $in_fh
  or warn "Could not close input file 1 '$input_file': $!";
close $out_fh
  or warn "Could not close output file '$output_file': $!";
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Or use this one-liner:

perl -wlpe 'if(!/^2/){substr($_,99,1,"9");substr($_,148,1,"Z");}' <in.
+dat >out.dat
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