What I think is what happened, that you have one server, if you disable it on the server, you can't hit ingame, and not in lobby, if you have 3 servers for example it'll work like this:
Server 1: (Can't use this server, it's the 'host' for bungeecord)
Server 2: lobby > you can disable hitting here, whenever you click a sign you get connected to a other server >
Server 3: Server 3 is the skywars game server, here you build your maps and stuff, here you enable PvP.
Hope this helped you out.
i dont understand srry