Essentially, the crux of the issue stems from the fact that when you add a server, the server is pinged to see if its available, the version its on and who's playing.
This allows users who have created bots that check hundreds of IPs a second to find private servers and destroy them. Most users do not know what whitelists are or how to make one, and putting the blame on people who thought they were alone is wrong.
A group known as The Fifth Column has a database of servers to grief, so even if you implemented some kind of non-discoverable box, it's possible such a database could be leaked and only half of the problem would be solved.
Because of this, I think the best solution is to have an effective, fresh backup system implemented. The design I have in mind is to backup a world each time a new user joins (unless the server is young or there was a recent world backup), and on a timer to save a player's loaded chunks into a backup database with server operators using chunk coordinates to load desired chunks back from a desired player's backup chunks. You need the chunk backups as there would be ways to go around the first system above.
You'd want to cut down on the size of these chunk backups. I'd compare saving blocks to the world seed and to mark those blocks to load from the seed instead of saving them to a file if there's a match, however this would not work cross-version.
But that's just my idea! Any other solutions in mind? Thank you for reading, I hope something can be done.
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