Do you know if the Atraxi & Prisoner Zero did still come? If they didn't, there's no question to answer.
If the universe was restarted without the cracks, then prisoner zero would not have been able to escape to earth and the atraxi would have no reason to come then. But since Amy is a time traveler now, she would still keep the memories of that time anyways. So just like killing madam kavorian, it did and didn't happen.