Despite her deeply engrained fear of Evil Flippy, in early episodes, Flaky seems to see Flippy as a friends as she not only occasionally plays with him and other characters but in Party Animal she goes though the trouble of planning him a surprise birthday party for him. This could be because the same episode implies that at that point she was unaware that they were the same person given that she very trustingly handed him the cake cutter which almost made him flip-out.
However, in Without a Hitch, she has definitely learned that and has become afraid of both versions of him. She not only tries to avoid him but throughout the episode, she has hallucinations of him flipping out and killing her. This fear goes as far as when he tries to help free her from the crashed car, she stabs him in the eye with a shard of glass. In her defense though, Flippy was coming at her with a potential weapon so she didn't really have time to look at his eyes or teeth to see if he was flipped.