In universe, Sophie was taking time away because Nate was, well, being Nate. Was there an additional out-of-universe reason that the role of Sophie Devereaux so minimized in season 2?
My initial assumption was that Gina Bellman was pregnant at the time, which would have been rather hard to hide in the normal flow of the show. Having her only appear on a Skype-like app would make it easy to hide a burgeoning belly. According to IMDB, she is married and does have a child. While there's no DOB for the child, her (only) marriage happened well after the filming of season 2, so I'll give her the benefit of doubt that it's not likely that was the reason.