ABC News began an investigation at the time, leading to Fernando's resignation, but no explanation was given as to how he ended up on the board.
Dozens of internal emails have now been released which appear to indicate that Cheryl Mills, a Clinton confidante then serving as the State Department chief of staff, added Fernando to the panel.
Citizens United, a conservative group, filed a freedom of information request to compel the department to turn over the emails.
When questions were first raised about Fernando's appointment, a press aide emailed colleagues saying: "It appears there is much more to this story that we're unaware of. We must protect the secretary's and under secretary's name, as well as the integrity of the board.
"I think it's important to get down to the bottom of this before there's any response," wrote Jamie Mannina. "It's natural to ask how he got on to the board."
A separate email indicated that Fernando was not on a list of potential board members sent to Clinton, but was "added at their insistence".
There was no response to a request for comment from Fernando.
Donald Trump, Clinton's rival for the presidency, referred to Fernando's appointment in a speech on Saturday. "They all looked and said where did this guy come from? He made a contribution of US$250,000 and all of a sudden he's on this very important and vital board," he said.
"This position dealt with tactical nuclear weapons and had top-secret clearance, and he knew nothing about it."
Trump was facing down controversy of his own after a report by USA Today detailed numerous instances in which he allegedly failed to pay contractors and employees of his hotels and clubs.
The report found that Trump had been involved in more than 3500 lawsuits in the past 30 years, many dealing with lack of payment.
