Ellis was convicted of 16 counts of child sex abuse in 1993.
This is his third appeal – the first led to one complainant withdrawing her testimony and three of Ellis' 16 counts of child sex abuse being overturned.
His second was dismissed by the court. He was granted leave for his third in 2019, but died months later after a battle with bladder cancer.
Ellis contended through his life he was innocent and the victim of a miscarriage of justice.
On Monday, his lawyer Rob Harrison told the court the appeal is hinged on a number of factors – firstly the risk of the children's testimony being contaminated.
He says the risk of contamination was underestimated, due to the lack of scientific knowledge about interviewing children in the 90s.
He says improper techniques were used to get information from the young children, and when the case did reach court in 1993 the jury were not "appropriately assisted by expert testimony".
"The jury could not decipher the information in the right way to reach a fair decision."
Harrison also says the children's interviews, upon which Ellis' conviction was hinged, were contaminated by a multitude of factors.
"Parent to parent conversation, child-parent conversations, official meetings, children overhearing conversations, booklet construction, scene reconstruction, therapy books and television."
Harrison says all of these factors could affect the recollection of children, or cause them to change their answers based on what they were overhearing or being told.
But the Crown denies the alleged contamination had an effect, saying it would be unrealistic to expect parents to keep their children in a legally sterile environment given the gravity of the accusations.
Jonn Billington QC says the considerable concern of contamination upon which the appeal hinges are "unreal".
"As this case unfolds you will see considerable concern of contamination which includes the parents speaking to their children during the process, that children underwent therapy, or had access to books about child sex abuse to keep themselves safe. In an ideal contrived situation, one might keep those children sequestered but the sort of complaints being made about contamination are unreal, these are little children whose parents love them and need to support them.
"It is unreal to suggest that conduct between child and parent contaminates evidence enough to disregard it entirely."
He goes on to say children should be taken seriously if they say they are abused - "especially if they are showing the signs that a number of other children of a similar age who were also abused have shown".
Harrison refutes this, saying there is no consensus on what signs or behaviours constitutes a victim of child sex abuse
"[There is] not one pattern or symptom that categorises the majority of sexually abused children."
The appeal continues.
