She realized that his “affection” was rooted in his desire to mold and possess her, rather than genuine care. It’s not that he’s dishonorable, he will still keep his word, but she knows that he doesn’t genuinely care for her as a person, but rather an accomplishment (he picked her up when she was destroyed and built her into a functional weapon to be wielded in high society). She still intends to work with him and keep her word, but she’s putting up boundaries to keep their relationship professional from now on.
She always knew that he was going to use her for political purposes, but their relationship was essentially a professional one between a boss and subordinate. He began acting more affectionate and flirty than would be required for their working relationship, so she started to become confused. Remember she has been in an incredibly vulnerable state for the entire time she’s known them. It’s not surprising that she would start to develop a dependency on the person who saved her and built her new identity.
I'm confused