The accused, who is above 50 years of age and is an athletics coach, is currently lodged in Tihar Jail under the POCSO Act.
Wounds and injuries were found on the child's private parts in the examination carried out by the surgery department.
The mother in the petition pointed out that the government notification on handing over the case to the CBI did not include the case number of the younger child's death.
In a judgement passed on January 19, the Bombay High Court had said groping a minor's breast without 'skin-to-skin contact' cannot be termed sexual assault as defined under the POCSO Act.
The woman said her husband had wanted custody of their son. When she refused, he had threatened that he would take the child away at all cost.
As per the statements of a 14-year-old girl, Dr Kailas was named as the third accused in a POCSO case.
The court directed her to furnish two sureties of Rs 1 lakh and also instructed her not to make any interventions that could influence the probe.
Though the couple had a love marriage, the woman has been living separately for the past three years owing to marital discord.
The girl who is now 17 years old, was earlier abused four years ago when she was just 13 years old and she was lodged at Nirbhaya home since 2016.
Drama artist Sasikumar masqueraded as an ex-serviceman and suppressed information about his marital status while adopting the girl with the intervention of the Council.