I don't know if someone already mentioned this, but from many comments I read, many were confused why the storyline changed.
When someone basically time travels in the past and informs about the future and tries to change it, he creates a time paradox.
That means that whatever had happened from that point till the future changes and the past gets rewritten.That's why when Neo wakes up he has a new past.
He told to his former self and senpai what happened and basically changed the storyline by making both of them realise they loved each other so they got together since that time in the past.
And so he should adapt on getting the memories he supposedly should have from the past.
But well, basically, this has to do with parallel worlds and possible futures which will make it even more confusing unless you learn more about time paradox theory ヾ(❀╹◡╹)ノ~
I hope this explained some part, but it'd be nice if you read that theory since it's highly interesting (● ̄(エ) ̄●)
Everyone seems so confused for some reason.
Did you read the prequel or started reading the sequel right away?
http://www.mangago.zone/read-manga/boku_no_kawaii_yopparai/
(づ ̄ ³ ̄)づ