Sources have confirmed the woman, 41, died last Thursday in hospital from an illness.

The woman and her husband were scheduled to appear before the County Court on Wednesday for a plea hearing over the death of their five-year-old son, who died on August 1, 2012, several days after he cut his big toe on an open tin of cat food.

The tin had been discarded in the house and was piled among junk, food scraps, mould, waste and faeces that filled every room of the house, in Melbourne's north-western suburbs.

The boy's mother and father, 43, both pleaded guilty to two counts of reckless conduct endangering a person and one charge each of failing to register the birth of a child.

The charges against the woman will now be withdrawn. The charges against the boy's father will remain in place and are expected to be heard later this month.

The names of the woman and man and their son are suppressed so not to identify the couple's other son, who was eight at the time of his brother's death. That boy is now in foster care.

The couple appeared before chief judge Michael Rozenes in July, when the woman fainted in the dock soon after formally pleading guilty.

Judge Rozenes adjourned the hearing so the woman could undergo psychiatric assessment.

In documents previously tendered to Melbourne Magistrates Court, the boy fell ill in the days after cutting his toe. The woman discovered her son lying lifeless in his bedroom and rushed him to an ambulance station, where he was pronounced dead, the documents say.

One ambulance paramedic said in a statement to police that the boy had grey, mottled skin when he was brought to them and that he had a filthy bandage wrapped around his foot.

Photographs of the family home, taken by police and also previously tendered to Melbourne Magistrates Court, show rooms filled with piles of junk and food waste, and mould and faeces splattered across walls and appliances.

According to court documents, the boy who died was born at home, was never immunised or enrolled in school or kindergarten and only really had contact with his immediate family members.

The boy's death will be the subject of a colonial inquest once the criminal proceedings are complete. It is expected the woman's death will not be investigated by the state coroner, as it was not suspicious and she was not in custody at the time. Her husband remains on bail.

The boy's death prompted an investigation by Bernie Geary, the principal commissioner of the Commission for Children and Young People, and details about the case were conveyed to the office of Community Services Minister Mary Wooldridge.