Fluttershy's first response is to flee. Sure, Twilight might not be calling the other pony Nightmare Moon, but she's still big and dark, with a starry mane and moon cutie mark.

She doesn't manage to get very far before Twilight's magic grabs on to her. She tries to resist, but it's really hard to get traction against magical telekinesis that can lift your hooves off the ground. Fluttershy is dragged out and turned to face the Princess. Still held by the magic, she tries to make the best of it. She summons a weak grin and weaker voice. "Likewise."

Maybe it's just some kind of greet-the-ponies event, and they'll let her go now?