I would put it a different way. The files were intentionally deleted by the contractor because that one person had no idea what the impact would be and how it could affect the entire system. This happens alot during system O&M.
The contractor randos should NOT have access to PROD.
That is assuming the FAA et al work that way. If the FAA simply lets a contractor have PROD access and make changes on the fly, heads should roll.
I heard a news story / propaganda piece where this failure was used to lament about the "antiquated" system and "more money is needed or else Bad Things will happen."