Why did Emilia have to be destroyed after compilation?, if he just made a back-up of her before compiling the payload, then he could have destroyed reaper and then recreated emilia. It isn't like file copying didn't exist on the Amiga.
(Answer taken from youtube) The only problem with that is the memory storage capacity on the Amie Workbench(42k if i recall). Seeing as Emilia was an AI, she most likely took a copious amount of data on the Player's computer/network. The computer itself probably just didn't have enough memory to handle two Emilias at the same time.]
Additionally, this is already answered by some of the in-game threads in The Underground Library. Long story short, Emilia's code won't allow for two Emilias on the same system, even if your computer could handle it; her code - and that of every other AI is set up to wipe itself when they move from one system to another. There's no way to save her, and she knows it.
You could still make an external backup that can't be destroyed, like putting it on a floppy and taking that out before.
A floppy would likely be too small to handle an AI copied on to it.
But the worm-deleting version wasn't the same code, and therefore, while it would delete itself, would not delete the code of the original, which could be re-compiled.
Hate Plus makes mention that the non-copying script has an absurdly large range, so it would still detect the copy.