The entire point of Al'Taieu being shifted was so that the Keeper of the Apocalypse would be sealed away. Thus, the Keeper would never arrive in Vana'diel, and no apocalypse would occur. You see this again in Apocalypse Nigh, where the goal is to defeat the returned souls before they can complete their incarnation into the Keeper of the Apocalypse (which was occuring because Prishe tossed her Magicite at Promathia; when Promathia was defeated, the Emptiness within the Magicite was returned to the crystal and was sought by the spirits of the various foes you defeated (Lion was protecting it from them.))
From what the various Lumorian NPCs say when you go to get the maps, it seems as though Bahamut had been attacking Al'Taieu, and the city's celestial defense mechanism kicked in and shifted the entire city into an extra-dimensional space. Said mechanism has been running for thousands of years, and the events of CoP begin when the events at the end of RoZ cause fluctuations in the crystal line that begin to disrupt the power source of the mechanism (the Al'Taieu mother crystal.) That begins the slow return of Al'Taieu to normal space.
As a side note, Al'Taieu was almost certainly located at what is now Qufim Island - the Sea of Shu'Meyo, which is where the portal to Al'Taieu is found, seems to cover an area that was practically scooped out of Qufim. Qufim and Al'Taieu have similar landscaping as well, odd coloring aside - the rock is similar, as well as the general appearance of the terrain.
As a side note, some Lumorian NPCs note that only the royal family can deactivate the celestial defense mechanism. One prince died at the Stellar Fulcrum, the other at the Celestial Nexus. The princess has other things to worry about right now. So no one's around who has the authority to turn it off.