I've toyed around with this a little bit and propose using the following format (starting around line 66 in your code)

 if ($aircraft_id_1 eq $aircraft_id_2){
    #print "$aircraft_id_1 eq $aircraft_id_2\n";
    print OUTFILE "$line_1;$line_2\n";
      }

      else { print OUTFILE "$line_1\n"; }
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and removing the earlier (line 45ish) print statement that only prints the line from the first file. This way you're figuring out all in one place whether or not you are printing just one line or several.

As best as I can tell your matching logic is fine. Or am I missing something?