The first appeal quashed three of his convictions.
The second appeal against the remaining 13 convictions was dismissed in 1999.
Ellis was granted leave to appeal those remaining convictions in July last year, but died in September.
The Supreme Court says the reasons for this decision will be provided at the same time as the decision is released on the substantive appeal.
Ellis's lawyer Rob Harrison said it was a great development in the fight for justice and chance to restore the reputation of his late client.
"I think it's fantastic news," he said.
"It gives us a chance to put before the court the arguments that we've been preparing for quite some time."
Harrison told Newstalk ZB's Chris Lynch once someone dies their reputation continues and there's a value to it.
"If the Supreme Court has gone down that particular path they're saying there's a value here that deserves to be respected and it means that there is valuing in continuing the appeal," he said.
The time frame for case was still unclear with a "tremendous amount of evidence" to be placed before the court and undergo cross-examination.
"We don't know exactly how long that will take and we will have to see what the timetable is of the court itself," he said.
He said the psychology in terms of memory and impacts of memory continued to evolve.
"What we knew back in the 1980s and 1990s has been further clarified since then but it's a massive area."
Harrison said it needed to be resolved: "In terms of our society as a whole I'm hopeful that
New Zealand always continues to evolve because we can't stay stuck in one place. What may have been acceptable 50 years ago is no longer acceptable. As a people we change our views, we move on."
He didn't want to comment further ahead of the case.
The Christchurch creche case
Ellis was released from prison in 2000, after serving seven years for abusing seven children at the Christchurch Civic Childcare Centre in 1991.
The verdicts have always been contentious and a year ago, the Supreme Court agreed to hear the case once more.
The approved ground of appeal was whether a miscarriage of justice occurred.
After the second Court of Appeal decision there was a Ministerial Inquiry in 2001 by Sir Thomas Eichelbaum, which concluded there was no risk of a miscarriage of justice.
There have also been unsuccessful petitions to Parliament for a royal commission in 2003, 2008 and 2014.