Don't you remember anything from Jurassic Park man? "Life finds a way. . "
lol, jk.
Really though, the planet isn't completely dead, or the Machines would be working on a way to leave. With sunshine, terraforming, and other as yet undiscovered of solutions, the surface could be revitalized.
Unless there is some official source that says otherwise?
With regard to humans and machines living together, it would take considerable tolerance and forgiveness (basically a whole lot of water under the bridge) to acheive, but it's not impossible.
Why would the Machines need to leave Earth if it were biologically dead, considering they aren't themselves biological entities? Tell me again what physical limits you think the Machines have that would require them to leave Earth even if it got really cold, or really hot? Or had no atmosphere. Maybe radiation would be a problem, but if the sky is blocked, I guess it isn't. We're talking about creatures made from software and hardware. Software can be stored on pretty much anything. Unless they've changed their design ideals their physical bodies are made up of parts designed to be replaceable, redesignable.. Machines are super adaptable, we are not. It's sort of a one sided doomsday. "The terraforming (literally, 'Earth-shaping' of a planet, moon, or other body is the hypothetical process of deliberately modifying its atmosphere, temperature, or ecology to be similar to those of Earth in order to make it habitable by humans." The art of turning what is, in our eyes, a dead rock into a living rock. I think your foot is bleeding. I do not doubt the Machines could terraform the Earth back into Earth, once we give them a clear view of the sun again. If we are lucky the Machines also cataloged the DNA of other Earth species, there might be a chance to recreate them. The Machines show much more tolerance toward us than we toward them. It's hopeful, but as the Machines pick up more and more of our bad habits... Or we push and push harder... Who knows.
There is no explanation for why the Machines have not shielded themselves. It may be that they've done it intentionally to make the fight seem fair to us. A form of control. If they look weak maybe we'll focus on them instead of rebuilding our strength. Explain how they can have fusion, hovercrafts(is that electromagnetic levitation?!), super lasers to cut through metal, etc.. And still not understand enough physics to shield against electromagnetic interference? The Machines surpassed our technological level a long long time ago, it's shown happening in the Animatrix. If you can adapt our current technology in the really real world to work under those extreme conditions... Uh, duh? If it's too cold for them, can't they just install heaters? Or just run electric current through the "skin" layer of metal. Like those heating wires that clear ice off the back window in cars. Sure, extreme heat would be a little more of a problem. But the sun is blocked. When they run out of resources to consume I could see them planet hopping.