A part of her actually expected and wanted him to use his sharingan, because that was the sort of training she was used to...but it was best that he didn't. Using her techniques against the sharingan would raise suspicions about why someone like her might have any experience with the sharingan at all, and potentially implicate Shisui as her teacher. So, that he continued not to use it was a good thing. She could practice her technique of cutting off his access to the sharingan while in genjutsu when she next had the chance to train with Shisui.

Still, she remained alert, ready for the inevitable reaction to her newest technique. Theoretically, he could leave the genjutsu at any time he chose to since this was only training. But he'd have to try much harder than that for her to determine he'd remembered his situation and wanted out. For one, she'd expect him to activate his sharingan, and for another she expected an actual fight for control when he wanted his freedom, considering the genjutsu skill Uchiha were known for, and how it was with her usual training.

This chakra flare she was prepared for, and rather than completely stand firm and risk slipping her grip or alerting him subconsciously to the resistance, she reacted much like she might to waves on a ship, shifting and adjusting the rest of his chakra network along with his flare of activity and then settling it back down when it passed. Within, presuming she got the timing and shape right (and she liked to think she did) the illusion should remain undisturbed.

Whatever was happening inside his mind, clearly the choice to combine threat and friend was the correct one.