Anything pushed to the "fediverse", if you will, can't be lost (except for images and other media). It's just that once an instance goes down, that instance isn't available anymore to push out new updates. So if someone replies to a post or comment that belongs to a community that "no longer exists", then that reply will only exist on the server of the user who posted it.
Based on what we saw when beehaw de-federated from lemmy.world, communities still exist on all remote servers that previously saw it, including any posts that were already there.
The only unknown is if those communities will exist indefinitely. I don't think there is currently any mechanism for cleaning up instance data but there might be in the future. It would be a good idea to have that as an explicit option for admins.
My old instance was deleted by the admin and all the posts are still possible to reach via other instances. Well maybe some got lost that maybe didn't get fetched by others, I'm not sure, but when I wanted to go back and save the posts that were "lost" they were there at least.