While fooling around in practice mode, I discover that if you drown a SuperLem, 99% of the time it will prevent you from assigning anyone else a SuperLem again (until you restart the level of course). While I haven't tested many other methods of killing SuperLems, I did test that merely making the SuperLem disappear off the level boundaries will not cause the same effect. I also haven't tested yet what happens if some other kind of transition besides drowning occurs (eg. what if the lemming has Swimmer ability? hmm, something to test next...)[edit: tested swimmer, same thing happens--can't assign SuperLem to anyone anymore]
[edit2: Further testing suggests a circumstance where the SuperLem will drown w/o preventing further SuperLem assignment, but it's even weirder. Basically make the SuperLem with swimmer ability nosedive fast into the water at a near-vertical angle. Even though if the SuperLem had swimmer ability, it will nevertheless drown! And yet, somehow with this kind of drowning which looks exactly the same, you can continue to assign SuperLem afterwards. Strange. Doing this with non-swimmer SuperLem doesn't work. Wait, it does.]
[edit3: I have a vague guess as to what might be going on with edit2. I'm testing this specifically in the Polar practice level with the relatively shallow pool of water at the top of the screen right over the first hill. I think if you dive the SuperLem into the water fast enough, if it's fast enough it will actually go straight from air to hitting the bottom of the shallow pool in a single frame. This is equivalent to crashing your SuperLem which will end the SuperLem ability, and only then does the game check for water and drown the lemming. So you bypass the glitch about not being able to assign another SuperLem, because the lemming actually drowned right after losing SuperLem as opposed to during. It's still a glitch thoiugh that this kind of dive would drown even a swimmer.]