It is currently a red-orange colour, the same as it was on the night Watson is believed to have murdered the pair after a New Year's Eve party at Furneaux Lodge in the Marlborough Sounds.
Mr Clausen told Fairfax that the production company wanted to repaint the Blade blue, to match the colour Watson painted the boat after the murders. Police say he painted the vessel in a bid to disguise it.
Watson's father Chris Watson, who owns the boat, allowed Production Shed to use the vessel because having it as part of a documentary was "good publicity".
He told Fairfax he was always willing to help "showcase the ridiculous way this case has been represented".
"The police and the courts did a hatchet job so there's nothing anyone can do that's worse than that."
Watson continues to maintain his innocence.
NZ On Air told Fairfax that neither Watson nor his family would be benefit financially from the documentary.
"The Blade has been repainted to its colour at the time of the disappearances for the dramatic recreations and will be returned to its pre-shooting state," the agency stated.
Mr Hope's father Gerald Hope said he had "no issue" with the NZ On Air funding.
"My greatest concern is that they represent the events and the facts surrounding Ben and Olivia's disappearance accurately and honestly."