I somewhat agree with Yautja here: if you're gonna make a story with time warping, anti-paradox measures and great mystery surrounding it, then you need to plan it very well beforehand, not just throw the damn thing prematurely and hope you will somehow make some sense of the story afterwards.
Also, the author completely forgot all about the small plot point of Chika telling the MC that she had a boyfriend and how she never cleared up that she had actually lied then (if the guy actually did learn of it, then please tell me when because I can't for the life of mine remember it).