The widespread adoption of generative AI in software engineering marks a paradigm shift, offering new opportunities to design and utilize software engineering tools while influencing both developers and the artifacts they create. Traditional empirical methods in software engineering, including quantitative, qualitative, and mixed-method approaches, are well established. However, this paradigm shift introduces novel data types and redefines many concepts in the software engineering process. The roles of developers, users, agents, and researchers increasingly overlap, blurring the distinctions between these social and technical actors within the field. This paper examines how integrating AI into software engineering challenges traditional research paradigms. It focuses on the research phenomena that we investigate, the methods and theories that we employ, the data we analyze, and the threats to validity that emerge in this new context. Through this exploration, our goal is to understand how AI adoption disrupts established software development practices that creates new opportunities for empirical software engineering research.