No, my rep did not carry over. I did get a rep bonus, though what exactly gave me the bonus I can't be sure. I had on a QW shader, emblem, and class item and I had the Nightfall bonus. My friend, who only had the emblem and Nightfall bonus, got the same amount of rep per turn in, so I'm guessing it's either the emblem, Nightfall, or both.
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It was the Nightfall bonus. I tested this idea with my warlock using the shader and banner from the original Queen's Wrath.