From your link
'Budowich made the revelation in response to a tweet from CBS Evening News anchor Norah O'Donnell, who said a DOJ source informed her the department was not in possession of the passports."
So no direct denial from fbi or doj, only 1!! Claim from 1 journalist
In addition, the only valid passport taken was a diplomatic passport which I would presume he is not entitled to. To whom do diplomatic passports belong?