That I wrote from experience of trying to edit lua files that I had been working after adding new landing zones, or larger formations, or objectives. While it is possible to do, there are a lot of opportunities for error (which I had done, over and over).It is essential you have completed your scenario fully before you create the .lua file as any edits afterwards to the scenario file (adding new units, changing objectives, etc) will require you to generate a new .lua file.
Not all edits will require you to create a new lua file, but major surgery in the scenario editor to a scenario might have it that it is required.