I'm not entirely sure what you mean by "Replaced", once a nest exists, it is that nest forever. it's only if you kill it, and the enemies create a new one that it might be a different nest.
And when I say A certain distance away from the start... I mean, when you travel away from the starting point, eventually you'll come across different nests. it has nothing to do with how far you've travelled, it's the equivalent of having to go to australia before you find australians. as such, in this game, the further away you go from where you started, different things start to show up, it's just a radius, literally measured as "Distance from start" as the transition.