[I find it stunning that someone so irresponsible could be entrusted to keep track of something so important.]
Really there are only two LIKELY possibilities:
1) It was misfiled and will turn up on a different shelf during a thorough search
2) It was pilfered by an insider and it will turn up at some point in the future after the person who took it can't be in jeopardy for theft anymore
The Apollo moon landing is arguably the greatest single event achievement of humanity to date and the original film of its happening would be a profound loss.