In Season 4, Judith remarried to her second husband Dr. Herb Melnick. In Season 6, she was pregnant with either Alan's or Herb's child. She gave birth to Milly Melnick in the last episode of the season, with Charlie sitting next to her.
In Run, Steven Staven! Run!. Herb reveals that he and Judith are no longer together after she caught him cheating on her with his receptionist. She took their daughter Milly with her, while Herb remains in their house.
Walden and Alan call her to come and help Herb in the episode Big Episode: Someone Stole a Spoon, she arrives and reunites with him.