Actually, it seems as though the lore dump the game gives you at the end says that the robots incorporated components of the human server within themselves, including the information remaining on the original Gestalt (Nier). The information on Yonah appears to have been old information from before Project Gestalt went fully under way. One interesting thing to note, the watcher symbol on Eve, the red eyes and the resemblance that the red girl (N2) sort of has to Manah/One makes me think the Watchers somehow influenced the machines as well, so they're a combination of their original programming, the information from the human server, and possibly some kind of inciting programming from the Watchers.
It'll be interesting to see if we can get a Grimoire Automata or something at some point to clear things up. Hopefully they realize that fans outside of Japan would be interested so we could potentially get a localized copy.