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.
Yes, it would be difficult to create a backup, but not necessarily impossible. Also, "Message in a Bottle" was the 14th episode of the 4th season as well as having a lower production number and "Living Witness" was the 23rd episode so "Message in a Bottle" probably happened before "Living Witness". Therefore, one could theorize after The Doctor returned, Tom and Harry were able to create a backup, perhaps with B'Elanna's and/or Seven of Nine's help thus explaining away the seeming discrepancy. Also, considering the events of "The Swarm", it's unlikely Voyager originally had an EMH backup. Hence, unless a backup was created sometime between the events of "The Swarm" and "Living Witness" (which seems unlikely to me), there would have been no backup to steal if we are to believe the Kyrians stole the backup program at some point before "Message in a Bottle" and little onscreen reason or at least little onscreen worry about the consequences of The Doctor's program being stolen, damaged, being away for an extended length of time, et cetera before the scenes with Tom and Harry in MiaB.