Doubtful the Knight Commander is anything like that. He's shown genuine concern for his own people, rewards/compliments competence. He asked for Fake by name to personally enchant his own sword, but I don't think he knows that the entire department has been slacking and dumping their work on him. I hope the investigation proceeds smoothly though, and the house of that shitty head of the department is abolished.
On top of incompetence and costing the Kingdom a major asset, I wonder what kind of other charges for criminal negligence can be filed for that fat fool.
As the fool isnt the head of the house and is no were near inheriting it, its unlikely it will hurt the house as they will probably just disown him. Sure he mentions his dads name, but it doesn't really seem like he is getting any actual backing and is on his own. At most the dad got him in the door for his current position, it does sound like he started at the bottom as least. So it wouldn't really be right for his failure to hurt his house. Now if they try to back him then it may, but I doubt they will.
It does sound like he used to be passable at least enchantment wise as he used to do the enchantments for the common soldiers, though were the previous higher ups are now is a question, did they get recruited away and just leave openings that let him rise up the ranks to the head? That's a mismanagement itself to have not filled the ranks and to just let all the skilled smiths be sniped away, or retire.
But yeah he is in a very dangerous position, if his family doesn't back him its him vs the knight order. The knights trust their lives the their weapons, to beat and abuse the one who supports them, to play politics with their lives. Yeah the knights will be pissed, and with the knight captain against him only the highest ranks of nobility would be able to cover for him as they can just report directly to the king, he might as well be a commoner if his family doesn't back him. Forget charges, without backing nothing really stands in the knights way from just slaughtering him. Who will investigate him vanishing, not the knights that's for sure. Even if he gets backing he undermined their entire military, he is very much screwed.