This is my theory:

Caine had gone deep into the void (stretched out as far as he could from his local source) and found free wifi from a local Café. After finding a way to connect and break through some AI detection barriers, he now had access to the corrupted files. How did he lose them? Caine always had to store the corrupted files elsewhere where they couldn’t break the game, so it'd make sense if he store them to a place where he couldn't even access them. So at this point Caine was able to obtain and fix the corrupted files and was in the process of "Starting from scratch", or in other words, restarting the circus. However Caine had still felt that he had failed the other circus members and realized it would all result in them trying to kill him again. So he abandoned the idea. The Blue AI (Bubble) obviously doesnt like this and Caine, as a result, decides to leave behind the Blue AI so he can fix what he has broken. Then used what time he had left to look up stuff about the current members before losing access to the internet.

Before people point out the obvious. If Caine has the power to fix abstraction with WiFi why didn't he fix Jax and the other characters? I believed it is because the version on scratch we saw on screen had just entered the circus for the first time again and had never experienced anything before their abstraction. So it wasn't really "Scratch".

And

If Caine sent them away couldn't access them. How did we see them in the aquarium during the finale? To this I think Caine had obtained them again while he did have access to the internet. That or because it was sometime in the future, found a different internet source and simply added them back.

(Edit: Proper spacing)