So let's say I created a brand new world. So far no chunk files. Then I modify the terrain or world in some way in chunk 34. A file for chunk 34 is created with my changes to the terrain. That kind of thing. And of course depending on how you dod things you can have a hodgepodge of things saved in files and generated on the fly. Of course, it's up to your own discretion as a developer. But I don't think everything needs to be saved into chunk files like that.