If JJ goes with the comics' explanation - that the Narada was retrofitted with Borg technology before its trip back in time - this could actually help the Federation if the Borg show up. We know that Starfleet got ahold of the Kelvin's sensor data on the Narada and used it to upgrade their own technology, so perhaps they've already got a defense against the Borg - even without realizing it. What better to defend against the Borg than technology which was, indirectly, taken FROM the Borg?
The events of the movie don't allow enough time for all the events in Countdown the comic to take place. However the DVD and Blu-ray special features do confirm the Narada was uprgraded at the Vault. So certain things from Countdown are semi-canon with the films.
Picard and crew's actions in ST:FC didn't create an *alternate* timeline, they merely fulfilled the existing one. Meaning: The Ent-E's participation in the events of 2063 was always supposed to happen. It's a predestination paradox.
So does that mean they were there the first time? It seems it would cause an endless loop in the timeline.
You got it.
Sorry sirs and or madams but the events of First Contact did create an alternate timeline. Very similar to the one that existed before but alternate.
The flow of time is a linear series of events of cause to effect. When you time travel you interject persons or things into a place where they had no existed previous. This can cause disruption in time's flow. Depending on the method used these can be large (Star Trek 2009, Yesterday's Enterprise) or small (FC or TVH).
What happens in First Contact is the Borg travel back to 2063 Earth and rewrite history in their own image. We the audience and the crew of the ENT-E saw this from the 24th century. Because the ENT-E was displaced temporally by the wake they were in they existed outside of time and were shielded from the effects. The was no first contact and the Federation and Star Fleet never existed.
So
Unaltered Timeline: 2063-TOS-TUC-TNG-DS9-GEN-VOY-2373 :Erased by Borg's Time Incursion to the past
Borg Timeline of Earth 2063-2373 now established.
The ENT-E crew went back to CORRECT what had been corrupted, and they succeeded. However they failed to prevent several people from dying and had to contaminate the time stream and give assistance and future knowledge to Zefram Cochrane and Lily Sloane. Not to trivialize these details but what was PARAMOUNT about this was ensuring Earth and the Vulcans made contact. This was the broad stokes of history that NEEDED to happen in order to ensure the Federations future.
New timeline: 2063(altered)-ENT-Regeneration-TOS-TUC-TNG-DS9-GEN-VOY-2373(altered).
However this is where the predestination/pogo paradox gets thrown around and it's incorrect. In VOY Year of Hell part 1 7 of 9 states the Borg were present at the events of First Contact. In VOY Relativity she states that the Borg traveled back in time where they SUCEEDED in conquering Earth, but that led the Enterprise following them back and changing the course of events. To which Temporal Star Fleet guy says "in a way the Federation owes it's existence to the Borg". Temporal Starfleet guy.. You're fired.
Had the Borg never traveled back to stop Cochrane the flght would've been a success regardless and the Federation would've been founded.
Relativity and Year of Hell part 1 where Seven brings up the Borg and FC are goofs on the sides of the writers. They were trying to be clever and witty but overlooked what was actually shown in FC. Ask yourself this:
1. How does Seven know the Borg succeeded? If Earth was assimilated in 2063 through 2373 then how does any record of that remain in the revived timeline where the Borg were defeated by the ENT-E?
2. Same question, How does Seven know the Borg succeeded? It can't be a predestination/pogo paradox that the Borg would both succeed in their goals (assimilating Earth 2063-2373) and fail at them in the same span of time 2063-2373.
3. Since the Borg never sent the message to the Delta Quad, thanks to Picard and Worf blowing up the disk. The DQ Borg had no knowledge there were Borg on Earth.
4. The ENT-E crew had the historical logs and the time frame of events of what should've happened down to the letter. The basically steered history back on track. However several people did die and Cocharane, Lily and their colleagues had all seen or at least interacted with the ENT-E crew. All of this is bound to leave impressions and change history.
There was only one timeline which kept getting changed by different parties. We see a similar event occur during ENT with the Xindi Sphere Builders and other Temporal Cold War factions. Everyone trying to supplant the past that exists in order to rewrite the future in their favor.
What we see in Star Trek 2009 is the thing we see in FC to an extent but more so Yesterday's Enterprise. The difference is no one was there to put things back the way they were before. Even when Spock, Kirk and Uhura of the altered time realize they are living in an alternate reality than the one Nero is from they don't try to change things to be what they should be. Rather they continue to live in the reality they do. Similar to how the ENT-D, her crew and Picard himself were all radically different in Yesterday's Enterprise. Time travel effect warp reality and it change their lives and destinies. Basically another time travel fiasco but instead they decide to stay in that reality and live through it.
The Prime Timeline still exists because Nero traversed time using a black hole. Theoritcally black holes are holes in space and by extension holes in time. Making his method more in line with Chaos Theory and Butterfly effect time travel. Where the smallest changes causes ripples through the timeline effecting the universe around it. Rather than String Theory or Linear time travel when events can be supplanted and rewritten.