Unless the infiltration teams upload viruses to destroy any traces of that technology, they they would have to backwards engineer what they had known from something they have on hand.
A) anyone who doesn't keep backups deserves what happens to them. I sincerely doubt that the "military-industrial complex" doesn't know that rule, in whatever era.

for a virus to pull of what your talking about, you'd also need to not only defeat any electronic defenses, but expose
all computer networks to it -- unless they're all connected to one giant internet, the ultimate defense of
not being connected should be useful. Again, assuming the people "in charge" have half a brain.
C) Computer viruses can't destroy whats in people's heads. And if the scientists involved don't know the results (not necessarily to the umpteenth digit) something is wrong. Sure, they may have to start "from scratch" but they'll know (in general) where to look, and what roads
not to take.
Edit:
Here, an example: imagine, please, trying to take away Aegis combat system from the navy. Ain't going to happen, is it?