Dina Wadia was only estranged from her father Jinnah becuase he did not want her marry a parsi like he had. He went through a lot of problem's because Rutti's father never approved of their marriage and it hurt him alot.
Ruttie's father always intervined and made their life difficult. Jinnah did not want Dina to be marred by the same problems, but Dina still wanted to marry her choice and Jinnah decided it would be best to not interfere in her life and let her be.
She did not move to India, her husband and his family were never going to move to Pakistan anyway becuase of their business interests.
Dina was with him when Jinnah was about to die.
Btw, Jinnah has family in Pakistan too, his nephews/nieces and their children still live in Pakistan.
Liaqat Merchant is a known family member of Jinnah who looks after his estate and this article of his details Jinnah's family and their where abouts.
Daily Times - Leading News Resource of Pakistan