While several witnesses could not say how the document ended up hidden away and denied it had been "buried", the last-minute discovery of a register prompted the probe to be suddenly halted to call new witnesses and bring others to face more questions.
The inquiry has now announced it will bring in Colonel Jim Blackwell – the former Director of Special Operations who, according to the register, may have had the file locked away.
It will also haul back three other witnesses - one who could not testify in person - to answer more questions about why they could not discover where the file had come from in 2014.
The inquiry last week also heard from former Chief of Defence Tim Keating, who denied there had been a conspiracy, but admitted to sloppy paperwork.
"It wasn't tidy, it was unprofessional, but it wasn't a conspiracy," he said.
The Defence Force told the probe its claims that civilian deaths could not have occurred were based on a misunderstanding by its top SAS office in Afghanistan and that it was not corrected until the discovery of the report in 2014.
The witnesses have been called to appear next month.