While the scene opened with Upton complaining about the thinness of New York pizza (in a callback to her similar complaint in the FBI crossover episode), the tone shifted when Halstead said they’d hit up a deep dish place when she got back, then asked her if she would be back.
Back in the beginning of the episode before Atwater got a target on his back for telling the truth, Halstead was on the phone with Upton, with Tracy Spiridakos making a surprise appearance on P.D. when Upton was busy teaming up with OA on FBI.