2387 is a bit of a problem for the current novelverse I imagine. You have the competing concerns of not being able to incorporate Bad Robot movie elements into them, while also being required to follow canon, which is essentially anything that occurs on screen. The only real way to make this work is to assume the events portrayed in 2009's Star Trek occurred, but just never actually reference them. This of course becomes a stretch when you consider it would mean ignoring the massive implications that would result from Romulus' destruction. Spock's disappearance can be more easily ignored, although to never bring it up would be a disservice to the character. It's no wonder that the novelverse has slowed down the march to 2387.
As Countdown isn't canon, I'm fairly confident the novelverse will simply ignore it.
Hearing about the destruction of Romulus I've been formulating a possible story in my head that would set straight the prime universe in an unexpected way. If I'm paid to write this. Not just once it's published and selling I'll do it. But I don't have time to get sidetracked without compensation right now. Abrams Universe is far too limiting writing out all the events that ever took place in it is the best way to go in my opinion. Tell me what you think.