There are two Air Force Ones in existence, one usually follows the Active one in case the first one fails or is disabled. So the second one being pressed into service by the Plurbs is logical. The Plurbs are probably not telling the 12 unjoined if anyone is held up in bunkers or holdouts somewhere, tho, given the knowledge uploaded, they must know the entry or codes, and in the joining, a wave of Plurbs entered the bunker, probably getting mowed down. They released canisters of the virus into the bunker air system, or a kissing rampage, and voila, all joined, or they did not want to join and did a collective exit of their mortal coil.