Lucia Chisnall (left) at aged 3 years and Darci Chisnall then 6 months old.
The once-boisterous little boy is affected so severely he is comatose in bed and fed intravenously.
There is no cure.
"He is like a floppy rag doll," said Mrs Chisnall. "There is nobody home."
Starship hospital paediatric neurologist Cynthia Sharpe, who treated the children, said there were only 250 known cases of ANEC worldwide.
Although the illness is not understood fully, experts have worked out that a viral infection triggers a "catastrophic inflammation in the brain".
"It's got a very high mortality [rate], and in survivors [causes] permanent brain damage," said Dr Sharpe. "That's very significant and because it's in the genes, repeated different viral illnesses can retrigger it."
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When Lucia was struck down with chickenpox in 2009, her immune system attacked multiple parts of her brain, killing healthy cells and damaging its ability to send and receive messages.
"She presented with a lazy eye and then she couldn't walk," Mrs Chisnall said. "That happened within a few hours."
Tobin Chisnall.
Steroids stopped the attack, and within a year Lucia was almost fully recovered.
But disaster struck in August 2010 when she contracted swine flu.
"She lost consciousness completely," Mrs Chisnall said.
The youngster was rushed to Starship's paediatric intensive care unit and put on life support. After weeks, the then 3-year-old was sent to the Wilson Centre for Children in Takapuna for rehabilitation.
"She was completely blind, completely mute," Mrs Chisnall said. "She didn't even cry for three months. And she couldn't move. She had to learn how to roll over and sit up and walk again - everything."
Another episode brought on by tonsilitis in 2012 affected Lucia's spinal cord and again prevented her from walking.
Mrs Chisnall, 33, said her daughter has the cognitive function of a 2-year-old. "She has terrible rages that she can't control. She's just tormented."
Lucia's condition meant that when Tobin became lethargic and unwell on Friday, he was rushed straight to the Starship, where he was diagnosed with swine flu.
An MRI confirmed that he, too, has ANEC and the once active, happy preschooler has been unresponsive since.
The Chisnalls brought Tobin home this week and his twin sister, Milah, and older sister, Darci, 5, are helping to care for their brother.
Tobin Chisnall aged 3 years with mum Sarah Chisnall in Starship Hospital.
Mrs Chisnall said her son's prognosis was unclear. "He was the cutest, bubbliest little kid. Lucia was responding much earlier, and he's not showing any signs of reaction."
They would now get their two remaining healthy children tested and consider immunisations against chickenpox and the flu.
A Givealittle page set up for the family on Tuesday night raised $15,000 in less than 24 hours.
Mrs Chisnall said she and husband Jared were overwhelmed by the support and thanks to the money, he can take time off work to help her to care for Tobin and Lucia.
Acute necrotising encephalopathy of childhood
• Only 250 cases worldwide.
• Extremely rare problem with immune regulation.
• Triggered by viral infection.
• Causes immune system to kill healthy brain cells.
• Has 30 per cent mortality rate.
• Survivors left with permanent and significant brain injuries.
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