I always thought they had a program for each choice, like one put them to sleep while the other one activated the tracer. Can't recall the exact lines but I thought they only did the tracer after he accepted meaning it was meant as needed for that step. Could really be either but I always thought the tracer program needed some signal that would only work when the host body received it, or a signal the body was being purged. They were all hackers so maybe they didn't need it but I assume they didn't see all the data from their view just what the machines let them to continue on the cycles.

I haven't watched the newest one and 2/3 are a bit fuddeled in memory so I may have easily missed a line, or other lore with it. Anyways just explaining how someone may come to this conclusion even if it's incorrect.