That's an interesting question. At the time being, I think the only way is to do regular backups and store them at a friends for example. That way an instance can be restored after the server has been taken.

Really the only way is to not save anything, or perhaps some sort of blockchain for all the comments and posts?

Blockchain is an interesting thought - or maybe something similar to Matrix. All instances have their own copy of a post and sync with each other. That way it doesn't matter if one instance disappears. Though, that would probably not comply with the Fediverse idea? Interesting thought experiment non the less!

I'm wondering if you use cloud based hosting what kind of protections you can get. For instance if you're running an AWS EC2 instance to host an Mastadon instance. Primarily running from outside of the USA, but utilizing Edge locations so the primary server hardware is not actually in the USA in this example.