Remove boss stones and boss altars before you upload the world on the server.
And put it back when you need it. There are couple of mods that can help you with this. I can help if you don’t know how.
But this will not solve your problem. I think the easiest way to solve your problem will be to change your “friends”
Or to force everyone to play with server characters mod - this mod will save characters on the server and players won’t be able to log in to other worlds.