When Saori opens up her Battle Skipper Voice Com to get out the AIES, it has the number 3 on it. But when she opens it up and takes it out, the number on it is 2, being animation recycled from earlier.
Since Todo left before the girls changed into their Exters uniforms, it would have been impossible for him to know Saori was one of the Exters.
If Todo and his group of soldiers were able to break into the base easily with no alarms, there would have been no reason for him to hypnotize Saori at all.