Responses
It did affect Yui's life, but only from the time he had initially met Amemori-san. Thus why he is re-living that entire time. Which I like that they are doing that, instead of dumping Yui into the same time he left at with no knowledge of how different his life was during the three months that he remembers being with Amemori, but now wasn't.

Nah, in theory, changing something in the past affects everything else exponentially. By changing Amemori-san as an infant, it changed every interaction he had in his life - different people, different events, etc., That little girl might not even exist in this new version. Following this theory, Yui's life should have been different as well. Time-changing story lines are complicated.