Changing an organisational hierachy is a bitch and if you have many parties involved cooking a bit of the main product, you have the classical miscommunication in parallel organized development, leading you to the point at which it is more work to figure out where things went wrong than to start all over.
If it's only magic that can help you, I'ld advise you to be honest with your customer and superiors and tell em about the flaws that cant be fixed, so you dont risk a lawsuit. You should at this point watch out for yourself, so you dont get dragged into taking responsibility for things other people have fucked up.
You should think about a quick master plan about where things can be wrong with the circuit within the limits of the things you actually can work on. And then allocate tasks to the particular member of your team, following the master plan that with the help of your team you can run some more tests on the chip.
In the end then you should give a detailed report on the tests you ran and either be able to have fixed some problems or tell that due to you not being able to change the hardware design, you couldnt pinpoint a special cause.
Especially with a thing like to keep a stable frequency in a ship, there are like a billion things that could have went wrong in the first place, which is like impossible to be solved in two weeks ( ranging from the material used, to magnetic distortions in the chip over hardware and software designs )
Your supervisiors shouldnt put you in a position like that, except they know you really can do magic.