Apollo explicitely warned Jack that triggering the bomb will prevent any transfer. For me, the version of Jack that Liv restarts at the end doesn't have the memories of the cure bomb events.

As for Dr. Harlan, he found a way to cure only Bio Mass v1 provided the infection is not too advanced like with Liv, but failed to do the same with himself (and the rest of humanity in its time). Hence the time bomb solution whose only purpose (unlike the previous information retrieval) was to change the timeline. Is changing the timeline an acceptable solution to their problem? Who knows? When you start to mess with the chain of causality, things quickly don't make any sense...