I think that this Hyrule is separate from all the others, like how in Wind Waker there was an old Hyrule from OoT that got flooded and a new Hyrule was built on a landmass discovered afterwards. I think that Hyrule ended (in one of the timelines) and the Zonai started another Hyrule on the land left behind, possibly after being directed to do so by their Godly ancestors to maintain the existence of Hyrule which they worked so hard to create.