The 10 stolen years is the reason the Post-Flashpoint universe is different from the Pre-Flashpoint one. They aren't 10 new years stolen during Rebirth, just a reveal/retcon about how they had been stolen all along.
Apparently, New 52 Superman isn't who we (and Pre-Flashpoint Clark) thought he was. With the current reveals, it seems like they're going in the direction that Pre-Flashpoint Superman is the true Superman of that world all along, while the New 52 was a placeholder of sorts, since he wasn't there during the reboot due to Convergence's ending. Although the actual real identity of New 52 Clark, after this reveal, hasn't been confirmed, so anything more is speculation.
Barry remembers Wally after meeting him and a preview for RedHood shows that Jason Todd has his post-crisis origin back, so it seems like there'll be some changes due to this reveal. The timeline won't line up perfectly, but I guess it gives them an excuse for the contradictions and plotholes that appear eventually.