Put a use strict in your code, fix the errors and then you will see:

This is my quick version. Note the differences:

my $ffdb = "ffdb.dat";
open my $fd, '<', $ffdb or die "open: $!";
chomp (my @ffdbdata = <$fd>);
close $fd;

print "Enter ID \n";
chomp (my $ID = <STDIN>);
print "Cant be empty!\n" unless length $ID;

open $fd, '>', $ffdb or die "open: $!";
foreach my $line (@ffdbdata) {
  my @column=split /\|/, $line;
  if ($column[0] eq $ID) {
    print $fd "$column[0]|", $column[1] eq 'IN' ? "OUT\n" : "IN\n";
  } else {
    print $fd "$line\n";
  }
}
close $fd;
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