I think it is unlikely that at the time of the Glamour being put over Golgotterath (the end of the C-I War) and the placing of the Barricades (perhaps soon after, perhaps at the same time, it's unclear) I think it is very unlikely that A&A were actually inside the Ark. In fact, Akka relates to us that the Nonmen might have thought all the Inchoroi were dead, although the Glossary tells us they were simply, "hunting the last of the Inchoroi into the deep places of the earth." Another spot liken the defeat as, "Inchoroi, whom they had driven to the four corners of the world in the days of Cu’jara Cinmoi."
In either case, we know that A&A survived and it is plausible that in the process of the Nonmen slogging through the Ark, A&A evacuate the place, realizing that the fight there was lost...for now and take refuge in Eänna. I think either the Barricades are a ret-con, or simply the Nonmen thought all the Inchoroi were really dead or so broken, that simply hiding Golotterath would be an acceptable solution. Only it wasn't, because A&A were still about, or so it certainly seems. As such, Emilidis later came and put up the Barricades, to make sure they wouldn't get back in, even if they found it.
The circumstantial case seems plausible, someone was out there, crafting the Tusk, appearing to Angeshraël, distributing the Chorae, but more importantly formulating this plan. I guess it is possible that this was done from inside the Ark, but that seems unlikely. Also, it seems unlikely that it would be Cet’ingira who would do all that, since we know nothing of his knowing the Glamours, or in general being that crafty.
Cet’ingira remembered the Inverse Fire and the Ark. And I think that probably, in no small part, A&A were apt to remind him, probably back in Eärwa, their work being done in Eänna with Siöl likely destroyed, along with the other mansions, apart from Ishterebinth. Emilidis was probably dead then too by some means, opening up more of a possibility to open the Ark back up again.
Also plausible is that post-Breaking, A&A returned to find the Ark. Thinking it was simply a glamour, they excavate, only to realize Emilidis wasn't so naive as to just hide the place, he sealed it. There is a big time gap here, presumably from about 0-525, so what they were doing, I don't know, possibly exploring options on how to get in the Ark. Possibly here is where they recruit Cet’ingira again, only to realize he isn't crafty enough, but maybe it is him who realizes who might be. Men, if only they could be taught.
In any case, we do know that, interestingly enough, it was Cet’ingira who was chief among those who wanted to begin the Tutelage of men, saying: "Let me make a ministry of the wisdom we have purchased with our doom. For among them are souls as wise as our own.” I think that fact that 252 years later it is he who shows the Mangaecca where the Ark is probably speaks to the duplicity in that statement. Cet’ingira had already been corrupted by the Inverse Fire, he simply hadn't lost his mind completely. Also plausible is that Aurang might have been whispering in his ear the whole time, hastening his fall into Erraticism. The wisdom he was set to impart wasn't the wisdom of early Nonman culture, it was the wisdom of the Inverse Fire, that damnation was coming and unavoidable, but could be fought.