Yes and no. Lecter likes her, yes, but he is also nothing if not true to himself. He's a manipulator. To truly manipulate someone, you keep yourself unpredictable and arbitrary when it comes to being kind and being scary. It's a well-known tactic of abusers and manipulators. Show someone kindness and cordiality, then suddenly shift to anger or intimidation. It prevents them from getting truly comfortable around you and they also subconsciously crave your kind and cordial side again, thus making them more susceptible to wanting to please you.

Yes, he was always civil, but he had no problem making her feel squeamish - he didn’t repeat Miggs’ utterance of “c*nt”, but still referred to it. He also countered Clarice’s “…sounds like something Miggs would say”, with “not anymore”, which obviously shook Clarice. And IF he was referring to Clarice’s period with his comment, it was with a “civil” euphemism as opposed to something vulgar.