aw check you nightwing, looking for sense in modern comics...
still i think it does have an effect on the timeline, it brings back the ol' zero hour paradox... let me explain as i understand,
if superman never went to the pocket universe, then he never gets ridden with guilt and never exiles himself to outer space, which means he never meets mongul or finds the eradicator, which means the eradicator isnt on earth to create the cyborg superman, and also the eradicator isnt there to ressurect superman after being killed battling doomsday. and since cyborg superman isnt created and mongul isnt aware of earth (i dont think) then coast city is never destroyed, and Hal Jordan never becomes Parallax, so the zero hour crisis doesnt happen!
and of course, due to the amount of times superman has saved earth, the earth will probably be smoooshed
Time is broken...52
I'm going to step away from current DC until the Crisis dust settles. A six or seven year crossover event is a little taxing on the wallet as well as the reader's geekiness.