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    foreach (keys %fhs)
    {
...
        {
        print $fh "#endif\n";
        }

for my $file (keys %fhs) {
    # ...
    print $fh whatever
      if $file =~ /\.\.new$/;
}

for (keys %fhs) {
    # ...
    print $fh whatever
      if /\.\.new$/;
}