Better yet, avoid the shell completely.

my $error;
for my $in_qfn (@in_qfns) {
   ( my $out_qfn = $in_qfn ) =~ s/\.(?:mkv|avi)\z/m4v/;
   system($handbrake => (
      '-i' => $in_qfn,
      '-o' => $out-qfn,
      "--preset=$preset,
   ));
   if ($?) {
      warn("Error converting $in_qfn\n");
      ++$error;
   }
}

exit(1) if $error;
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