Procedural Generation & Avoiding the Butterfly Effect

This is a general question / request for advice on maintaining a procedural generation system through multiple post-release updates, without breaking previously generated content.

I am trying to find information and techniques for avoiding "Butterfly Effect" issues when creating procedural content for games. When using a seeded random number generator, a repeating sequence of random numbers can be used to create a reproducable world. While some games simply save the generated world to disk once generated, one of the powerful features of procedural generation is the fact that you can rely on the reproducability of the number sequence to recreate a region multiple times in the same way, removing the need for persistence. Because of the constraints of my particular situation, I must minimise persistence, and need to rely on purely seeded concent as much as possible.

The main danger in this approach is that even the slightest change in the procedural generation system can cause a butterfly effect that changes the entire world. This makes it very tricky to update the game without destroying the worlds that players are exploring.

The main technique I've been using to avoid this problem is to design the procedural generation in multiple phases, each of which has its own seeded random number generator. This means that each sub-system is self contained, and if something gets broken it will not affect everything in the world. However this seems like it still has a lot of potential for "breakage",even if in an isolated part of the game.

Another possible way of dealing with this problem could be to maintain complete versions of your generators within the code, and keep using the right generator for a given world instance. This seems like a maintenance nightmare to me though, and I'm curious if anyone actually does this.

So, my question is really a request for general advice, techniques, and design-patterns for dealing with this problem of the butterfly effect, especially in the context of post-release game updates. (Hopefully that's not too broad a question for SO.)

I am currently working in Unity3D / C#, although this is a language agnostic question.