The couple has split and the kids - Ruhi and Aditya have been also separated
http://www.bollywoodlife.com/news-gossip/yeh-hai-mohabbatein-will-raman-fight-for-his-sons-custody/
When they decided to split, Shagun took Aditya with her and enrolled him in a hostel. Ruhi stayed with her father and her grandparents. After fighting a legal battle, Raman officially got the sole custody of Ruhi, but his ex-wife's boyfriend, Ashok (Sangram Singh) told him that Raman's daughter is his and Shagun's love child. Raman lived with this doubt, he doesn't want to get a DNA test to confirm the paternity coz he feared upsetting his parents. Will he ever find out the truth about Ruhi's real parents? Who knows!