We lose the communities from that instance, yes. And that’s why people want to make sure you don’t have one dominant instance on the threadiverse. But frankly that issue will be there unless you have a fully decentralised system.
That being said, other instances will have a cache of the activities happening on this other instance. You can then fairly easily recreate it from this cache, and if you have a lot of storage, can also have a limitless cache.