If you don't want to use the Single Instance Server, just comment the lines (or add a condition) in the addSingleInstanceListener, removeSingleInstanceListener and callSingleInstanceServer methods of the StandaloneSingleInstanceService inner class of SweetHome3D main class.
Note that if you disable this feature, you won't be able to copy paste items between launched application instances.
Please, explain why you want this behavior. If it's interesting, I could add a system property to disable the Single Instance Server.