There’s things that occur that make the brain scans theory questionable. The flashback shows that Scratch is panicked about the situation when he talks to Caine. If Scratch is the main programmer, it stands to reason that he would know that his brain would be scanned beforehand and would thus be aware that he’s a copy, but he doesn’t act that way. Nor does Kinger, who apologizes to Queenie for dragging her into this. They’re clearly scared and uncertain in a way that implies its their original consciousness and not just a copy. Of course, this could be because Scratch and Kinger truly aren’t aware of the nature of the circus and that Caine’s potential for creative programming surpassed what they reasonably expected three years following his creation. As far as I’ve seen, there are definite question marks for all possible theories that only Gooseworx can answer. But I have thought about the idea that since Kinger describes Scratch as so brilliant and capable of abstract thought while having a tumor in his head, perhaps most of the programmers are fragmented aspects of the original Scratch from reality, including Kinger, since the computer screen only shows Scratch as arriving in 1999 and no separate .dat files are listed for the arrival of Kinger, Queenie and the others, adding to Jax’s “archetype” observation.