Chip,
Sorry to hear of the problem. I know that sinking feeling when mine leaked a few years ago. Quite a task to find and patch but mine didn't go anywhere near low enough to damage the liner. A few slits in the deep end. Never did find what caused them. The only way water would come out the waste line is if the discharge is lower than the pool, and now, lower or equal to the present water level and siphoning occurred. Should be easy to find with only 3' of water left. I don't know for sure but I wouldn't suspect any problems with the walls due to lack of water unless ground water is pushing on them. If the level is still dropping you probably have a leak at the drain itself. If you want I can dig up some threads where I've posted ideas using dye to find leaks.
Al