Actually, the only one who remembers events like that is Power Girl.
Everyone on the JSA, from Earth 2, have vague recollections that there was a multiverse but that's it. DCU history is nearly identical to what it was.
Why is Power Girl the only one with real Earth 2 memories will be explained in Justice Society of America. I think some confusion has come from interpretation of interviews more than the comics themselves.
Hippolyta was a member of JSA, Matrix Supergirl did exist, Etc.
Thursday, September 21, 2006
So Polly did take a Time-Trip
On the Newsarama thread for EAglesham's interview, Geoff Johns showed up to clarify some things (this thread pointed it out):