Is there any in-universe explanation for this change from the way the universe seemed to be in Civil War?
We just don't have any information as to why Pepper and Tony are back together. They just appear to be happy again.
All we know is that they were "on a break" during Civil War because the the producers/directors wanted Tony to be "off balance" for that movie.
"The intent in this movie, because we knew where we were going with the character, [was] that we had to motivate Tony to want to kill Bucky Barnes in the third act in order for the third act to work correctly, that Tony would have to be off-balance," explains Russo.
"The way that we thought we could make him off-balance was by pulling things out of his life, making him emotionally vulnerable. Really emotionally vulnerable," he continues. "So, Pepper is out of his life. It clearly is an issue for him, as you can see, by Robert's performance here."
In Civil War, Tony told Cap that he and Pepper were on a "break" because she felt he was too obsessed with his work as Iron Man. He hoped that signing the Sokovia Accords would be a good compromise and help keep him in line for her. It's unclear whether or not Pepper is actually in favor of the Accords, though given the final act of Civil War, it would be surprising if Tony himself were still totally on board.
Presumably the in-universe reasons for Pepper's absence no longer apply (or she just shrugged her shoulders and forgave him).