@Marchimarch@PawPadKnight don’t think it’s that because if he killed her he would have seen the eyes already.
My guess is that’s the time both of them made that conversation she’d greeted him that way 564 times and that’s how many times the girl has restarted and technically died after someone confessed.
@greatninja3 They probably meant he confessed 564 times right now, having guessed the method from Makoto's discussion with the other guy. Your theory is possible as well, but his shocked look and that small black panel to indicate time passing make me think something happened right then.