Flores called in Dr. Mark Korson, chief of metabolism. Justina's sister, Jessica, had been diagnosed and continues to be a patient of Korson, according to Pelletier. Justina was similarly diagnosed with mitochondrial disease. Korson treated Justina with a vitamin cocktail and various prescription medications.
When ABCNews.com called Korson and Tufts Medical Center for comment, they declined, citing patient confidentiality. Korson and Flores are also prevented from speaking about the case because the court's gag order.
Mitochondrial disease affects the body's ability to make energy, according to Dr. Richard Boles, medical director of Courtagen Life Sciences, a genetic testing company in Massachusetts, and a practicing physician in Los Angeles.
"The symptoms can affect any part of the body," said Boles, who did not treat Justina. "It can cause just about anything. People with mitochondrial disease can have diabetes, autism or other types of retardation, seizure disorders or migraine, chronic fatigue or intestinal failure."
"People with mitochondrial disease have a lot of pain," he said. "Normal sensations are amplified by the nervous system. They are not making it up. The idea of somatoform is you are making it up to serve some need. But they are having real pain."
The disease is variable in its severity, and treatments include high doses of vitamins, antioxidants and stress reduction, according to Boles. While diagnosing the rare disease used to be controversial, doctors now have genetic tests to make clearer diagnoses.
He said he had a number of patients who had been previously diagnosed with somatoform disorder or Munchausen by proxy by "a well-meaning medical team" before he discovered they had mitochondrial disease. Munchausen by proxy is a psychiatric condition in which a caregiver, usually a parent, seeks medical attention by exaggerating, making up or even causing a child's illness.
Justina seemed to be doing well on treatments for mitochondrial disease until February 2013, when she got the flu," according to Pelletier. "When you have mitochondrial disease and get sick, it hits harder."
Justina was in pain and had stopped eating, so the family called Korson, who recommended Justina see Flores again, who by then had moved to Boston Children's Hospital, said Pelletier.
She was taken by ambulance to Boston Children's on Feb. 10 and seen by a young emergency room doctor, who Pelletier alleges told the family that he "didn't believe" in mitochondrial disease. "For the first couple of days, we were open to trying a new approach," said Pelletier. But on Feb. 13, he alleges "reality started to strike."
"She had been there three days, and doctors had not had any conversation with Dr. Korson," he alleges. "They had not looked at any page of her medical records from Tufts."
On Feb. 13, Boston Children's presented the Pelletiers with a treatment plan for their daughter, which explicitly excluded input from other doctors outside its own medical team.
Since then, Korson has been an ally of the family –- "one million percent," according to Pelletier, testifying in the court appeal. "He's been crying on the phone with us."
ABCnews.com obtained a copy of Justina's treatment plan, which was described as: "multidisciplinary, team based; positive, proactive, forward looking rehabilitation-center, therapeutic approach rather than diagnostic."