Nonsense. I have always used XOrganiser for manipulating my scenery_packs.ini, did so with the Orbx files, and it saves them without problem.
It doesn't necessarily put everything in the correct order but it makes moving the entries around so much easier. Instead of cutting and pasting it is simply a question of moving an entry from one box to another. Then, so long as autosave at the top is "on", it writes it to the file. And I would have thought that a red bar telling you there are incorrect entries would actually be helpful so you don't waste time firing up the sim. Then you just ensure everything follows the correct order as Admiralty013 states....it's hardly rocket science!