I read where Johns said the new Earth-2 isnt the same as the old one but upon re-reading the first annual and a few JSA issues it looks to me like they are one and the same.Same history right upto COIE which they remember so I must be missing something.Will someone tell me the rest of the story and what books and issues to find it in?
It is absolutely a new world - the history might be aligned with the old one but this is a different world. At the end of 52 there were also other Earths with the Charlton, Fawcett, Elseworld and Captain Carrot characters present. Rip Hunter and Booster Gold literally saw it being born when they prepared to face Mister Mind in the end of 52.
Timelines might realign on their own and the new Earth-2 may well have the same history as the old one; in Legion of 3 Worlds the adult Brainiac from Earth 1 tells the one from Earth Prime that it's the Earth 1 Supergirl who has been visiting his (alternate) Earth, and that time travel often sends people to other universes. Hence if people can traverse universes timelines and events can too.