This may be a little difficult to grasp but hang on....Good luck!.
Although the timeline has changed in the new Trek movies there is a constant that cannot be avoided which is based on various time travel theories.
Now since Nero came through the wormhole and destroyed Vulcan after Khan came into power means that history had not been changed up to the point where Khan nearly becomes the ruler of Earth which lead to the events in the newest Trek.
The events surrounding the V'ger (Voyager) Probe and the Whale Probe would also still be present because both of the events that created these two events further along the time line occurred long before Nero showed up and changed the past. In fact both events which would be the launching of the Voyage Probe by NASA and its disappearance and the extinction of Humpbacked People occurred long before Khan came into power. With that in mind based upon time travel laws the V'ger Probe should be making its way through space enroute to Earth looking for the Creator as well as the Whale Probe making its way to Earth to question the disappearance of the humpbacked people. Both should make for very interesting movies to then branch the movies off into a new timeline.
Although the timeline has changed in the new Trek movies there is a constant that cannot be avoided which is based on various time travel theories.
Now since Nero came through the wormhole and destroyed Vulcan after Khan came into power means that history had not been changed up to the point where Khan nearly becomes the ruler of Earth which lead to the events in the newest Trek.
The events surrounding the V'ger (Voyager) Probe and the Whale Probe would also still be present because both of the events that created these two events further along the time line occurred long before Nero showed up and changed the past. In fact both events which would be the launching of the Voyage Probe by NASA and its disappearance and the extinction of Humpbacked People occurred long before Khan came into power. With that in mind based upon time travel laws the V'ger Probe should be making its way through space enroute to Earth looking for the Creator as well as the Whale Probe making its way to Earth to question the disappearance of the humpbacked people. Both should make for very interesting movies to then branch the movies off into a new timeline.