Didn't the prime intellect already wipe out 100% of humanity during the change or whatever it was called? Unless that was what you were talking about. The second wipe was to bring a at least a few people back.
PI just digitized the universe, like converting a mound of VHS tapes to digital. If they were really dead it wouldn’t have been possible to reverse it.
Did it also digitize all humans so it can have more control preventing death?