now that is another point. preexisting structure is part of generation, so removal would need to be saved for that. What I am saying is that any changes need to be saved, default state should not. SO the more you change the bigger it gets. If discovery also ups it, I got nothing... not sure what it could be doing in areas you didn't touch but just walked through. Killing anything is probably a change, though, and starts the spawn timers and so on.
I think I want to change my answer :)