When you rescind consent it doesn’t apply retroactively. If you give medical power of attorney to someone, they okay you for heart surgery, and a year later you take away the power of attorney from that person it doesn’t mean the heart surgery was done without consent. Same thing here; resigning from operative status doesn’t mean SAINT has to undo whatever they did while you were legally under their power, but it does mean they have to stop.
As for training time, it can be increased if you want it two, but I was just basing this on real life: New Agent Training for the FBI lasts twenty weeks as well and they come out the far end as full Special Agents. In this case, INDOC is twenty weeks of specialized training on top of the previous year of Basic Training for all Star Army personnel and the four weeks of SELECT.