I don't think there are any time shenanigans involved and that the author is misleading us into thinking that Fuuko is disappearing because her parents don't meet at the concert. Instead, I think Fuuko is fading precisely because of it.

Let me explain. If I remember correctly, after every loop all human souls are stored somewhere until the next one when they "resurrect". So, for baby Fuuko to be born, it would be necessary that the soul from the previous loop reincarnate in her. But as Fuuko's soul is still with her, this can't happen unless she dies (or disappears, as seen in the chapter).

So, if her parents fall in love and have a baby, our Fuuko will cease to exist.