R. Star wrote:
Really the concept a computer program can't be -copied- is silly anyways.
A program, sure. But a sentient consciousness is not a program, it's an emergent process. Even if you did copy the basic programming that defined its substrate level of activity and replicated its initial conditions as closely as you could, the mind that resulted when you actually ran it wouldn't be quite the same as the one that emerged the first time -- just as if you run a complex enough simulation more than once, you can get different results each time.
Also, if the Doctor's consciousness is based in quantum computing, then it probably wouldn't be copyable. Measuring quantum state information precisely enough to replicate it elsewhere -- i.e. quantum teleportation -- destroys the original information, due to quantum conservation laws.
So really, the Doctor having a backup at all is problematical, given that he was otherwise consistently portrayed as being unique, only able to be moved from one computer or emitter device to another rather than being copied. And in the later "Message in a Bottle," I think it was, Tom and Harry were struggling to create a backup as if they'd never had one before. So it's a tough episode to reconcile.