For such a key story element, they sure get their stories mixed up about Prime Base and the Backup Prime. For instance, 3rd edition says the Backup Prime staff is all in "cold storage". 4th edition states that Backup Prime is smaller, with relatively few frozen specialist in addition to the "awake team".
So 3rd edition, with Backup being frozen you can make a case for it not activating the Project in a timely manner. But in 4th edition, Backup Prime has staffers awake. No reason they can't be in radio silence with Prime Base broadcasting updated after the bombs fall to keep them current. But that would mean they would be aware of any problem at Prime Base and could start working up contingency plans.
There has to be some version of the story we agree to about the fall of Prime and the normal operational status of Backup Prime. Otherwise it is just a lot easier to just say, "There was a problem and the wake signals never got sent" with no attempt to explain it.
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