Short answer: No fragging clue.
Long answer: That is just one of several things that keeps me believing that Deus (and possibly Mirage and Maegera) is still around someplace, though hiding. The fact is, there is too much we don't know. The events during the Crash itself, especially those on the floor of the ECSE, didn't exactly get recorded reliably. Given all the isolated places one could keep backup copies, and the fact that everything that has ever been on a computer, going back to things before the first Matrix, can be found in the Endless Archive, it isn't unreasonable to say that, without doing the digital equivalent of finding the body, chopping it into little pieces, burning it, throwing it through a wood chipper, and salting the earth where it falls, the big three AIs could have survived. All we know is "Well, we haven't seen them since the Crash, so they must be dead."