If it's a @addwarp, I think @unload delete it completely.
Killing it comes to the same as @unloadnpc but you don't need to seek out the warp's name with @mapinfo3 (not sure about that command, I'd need to check).
If all else fails, you can use @reloadnpc, but I don't recommend it as it resets your server and may cause a lag spike to your players.