In my singleplayer survival world, I built a large underground base, and stupidly decided to put my nether portal in it at about y=10. I ended up being stuck in a nether cave underneath huge amounts of lava. I built another portal on the surface, but since it's within 128 blocks of my first one, it goes to the same place.
If I place water next to the lower portal to deactivate it, if I then use the surface portal, will it take me to the surface in the Nether? If not, what should I do?