After 8yrs of Obama and from what we have recently seen, that is a legitimate question.
Almost certainly, there have been back channels up and running that will help id the good guys in place. Not all the admirals and generals that continued with Obama's outlandish policies were bad guys but rather some sucked it up saw the need to remain.
Worse case, Trump can work his way down the chain of command until he gets the one he wants (or the one Rudy recommends). If not, he can bring in someone or even a team he has good reason to trust.
How does the DOJ define subpeona? Isn’t it give us something when you get around to it if you haven’t lost it already. You can ignore it if you want or just blacken out any info that might incriminate you.