The reload command can lead to data loss, but it does NOT harm cubedcraft. So why not just activate the command? it makes life drastically easier. It's just annoying when you have to restart the entire server every time.
Small addition: You could just give a warning instead and have to confirm that you really want to reload the server.
When you add a plugin from the panel it doesn’t get added right away, all plugins get added when the server starts and then removed again, the plugins do stay loaded