If you were actually trying to reconcile the myriad of continuity problems that exist in Star Trek now, a future temporal war changing history isn't the worst way to do it. I mean it'd probably be better to just ignore it, but if you had to explain it.
In a similar vein, I used to have a theory that Enterprise (the show) was a result of the changes to the timeline caused by the bits of future knowledge Zefram Cochrane learned in First Contact.
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