the twelve city states

[Enkidoh]

So your 1.0 manual text is different to the history text in the encyclopaedia 1 -

No, I never stated that (and for what it's worth the Lorebooks do retcon some things - Nael's gender is an example). What I was explaining is that there have been different city-states rising and falling in Eorzea throughout history, with each Calamity especially often resulting in new societies rising from the ashes of the old. Hells, even in the Sixth Astral Era the city-states that intially formed after the flood subsided was somewhat in a state of flux throughout the nearly 2000 year time span of that Astral Era so that most that existed at the start of that Astral Era, were not the same ones when Bahamut blew his way out of Dalamud: Gelmorra gave way to Gridania, Belahdia split into Ul'dah and Sil'dih (with Sil'dih later being wiped out), Avalonia was replaced by Ishgard, and Sharlayan founded a colony in Dravania that they later abandoned when the Garleans annexed Ala Mhigo. So it has been since the beginning of time.

There was undoubtably other city-states that existed prior to the Fifth Astral Era ones (the ones that would have existed back in the Third Astral Era would have all been hammered into the Allagan Empire though), although whatever traces or records of them probably no longer exist, with any records from those eras that do are probably locked away in Sharlayan's libraries, and it is that that I was referring to.

Also it is important to remember that there are actually aknowledged errors in the books, mostly due to changes in the lore that were made with recent content added, but these are only small points and don't discredit the books as a whole (and that is not even taking into account that the books are actually written from the point of view of in-universe scribes, who may not have all the 'facts' themselves). It's just something to be aware of.