I actually think his New 52 timeline as we know it will be almost completely erased.......and it'll make PERFECT sense in relation to the New 52 Superman's story.
Here's why: so, I don't know if you read Morriosn's Action Comics or not, but in it we find out that the reason Superman's life was changed even beyond Flahspoint's influences was because of Mxy's rival named Vyn. Vyn went in and basically killed the Kent thus setting off a domino effect in Clark's life that made him into what he was for better or worse. Though, it is made clear a number of times in the run that Clark could've and more than likely would've been something almost completely identical to the Pre-52 Superman had Vyn not killed his parents.
This is a vision of what Nuperman wished his life was like back in Morrison's run. Notice how the basics are FAR closer to Pre-52. The only think that's really changed are the aesthetics (ie the suit and the look of his friends).
I'm thinking that going forward we're going to have a past that is closer to this ideal version ie the Pre-52 one because that's what his life would've been without Vyn's attack.
So ihe wouldn't even remember his New 52 life as anything. He'd have his new/old idealized pre-52 origin.