I haven't played yet, just saw on the Catman stream, so I may be way off base here and might need to amend my post. So basically if I'm full of shit feel free to ignore this.
From what I gather you are saving all the terrain data to disk. Why? The beauty of procedural world gen is it can be recreated at anytime with a seed. Have each chunk represent a seed in the terrain gen and load them that way.
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.
