In that era of Flash comics, time travel was shown to be cumulative, rather than one self-consistent timeline where all instances of time travel were pre-destined and accounted for.
That's how we had one timeline where Nora died in old age of natural causes, and another where she was murdered by Reverse-Flash.
Barry's revival itself is another change made by the Reverse-Flash. After his revival in Blackest Night, he went back and revived Barry during the time of Final Crisis. The Final Crisis and Blackest Night we read are not those of the original timeline. In theory, there would be a Final Crisis and Blackest Night in the "Nora lived" timeline, that Barry didn't participate in, but did lead to Reverse-Flash's resurrection.
Iris had returned to the present day long before Final Crisis. So when Reverse-Flash revived Barry, the Iris West he was reunited with was the Iris West who had raised two kids in the future.
It's at this point that Barry could choose to go to the future and raise those kids with her. Doing so would create a new timeline. It would change the history of the Iris he had just been reunited with. In turn, this would also change the history of everyone Iris interacted with after she returned from the future.
Is this something Iris would want? Would she want the past 25 years or so of her life to be overwritten?
(At the time, all a bit moot, since they'd decided that positive Speed Force users couldn't change the past, only Negative Speed Force users.)