Would Shedinja be able to survive primary damage like Flamethrower, or at least secondary damage like from the effects of Life Orb or Double Edge?
Substitute does not block recoil from Life Orb, sandstorm damage or attacks such as Flare Blitz anyway and Shedinja is not any exception. Shedinja would get the standard protection from substitute if it's baton passed to it. The only thing is that it cannot make a substitute itself.