Could the system's timezone change? Yes. If you're manipulating time sanely, you're already using a timezone aware time class - particularly when serializing - and that's great. But if you're uncertain, it's best not to try to rectify. Your program will never be able to guess with any success.
Almost all of this post strikes me as along the vein of the questions of Babbage - "Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?" Almost all of these are the wrong numbers. Rather than leading you to the simple, correct solution (Use good serialization formats and timezone aware datastructures) it leads you down a path of paranoia, convinced the world is out to get you. If you're programming for that world, you're either a DRM programmer and should burn in hell, or you're doing it wrong. Trust your environment and OS and make damn sure that when you're setting up those layers you set them up right - Don't worry that every second open() call will return an invalid filehandle, just because.