Honestly, I doubt it will ever even become an issue. The Abrams films are now safely off in their own timeline, and it's unlikely we'll see any new televised Star Trek
until they're done.
And, frankly, if I were to bring Star Trek
Prime Timeline back to TV -- and Leonard Nimoy said in a number of interviews promoting ST09 that he thinks the film was so big that Star Trek
can never go back to TV anymore -- but, if I were to do it, I'd do another TNG-style time jump and advance us to somewhere in the mid-24th Century. Plenty of time for clever authors to reconcile the Destinyverse 2380s with whatever I introduce. Obviously that's just me, but I do think that the creative advantages of such a time jump -- that you'd be generally free to both play with the same basic toys (the Federation, the Klingons, the Romulans, etc.) but also free to establish entirely new relationships among them -- are pretty obvious. There's a reason Gene put TNG in the 2360s rather than the 2290s.