You could put the file-names to keep in an array. Perl will waste a bit of space on empty slots, but so long as the largest number is not huge it should be efficient.

my @filenames
foreach my $file (@files)
{
  if( $file =~ m:/file-(\d+)-2.txt$: )
  {
    $filenames[$1] = $file;
  }
  else
  {
    warn "Unexpected file found: $file\n";
  }
}

foreach my $file (@files)
{
  print $file if defined $file;
}
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This method will silently discard duplicates, which may or may not be a problem for what you are trying to do, but it will be fast.