I've treated both gigantea and magnifica many times and I just completely drain the tank with the nem inside. In the wild, during low tide, they are sometimes completely exposed to air, and are even in positions where they are hanging off of rocks.
It's important to remove as much water as possible to minimize the pathogen that's causing the infection.
I typically use freshly made salt water for my water changes. My main tank has gigantea in them and I prefer to use water that isn't exposed to any type of chemical allelopathy. It's likely that there isn't anything in the water to affect a sick nem, but I always try to remove any possible contaminant.