Question about the VNs' endings.

So I have finished S;G and just now finished S;G0's Recursive Mother Goose's ending. One thing I can't get out of my head is that how exactly do they change the world line by affecting the present? For S;G's case they changed the present by deleting the message from SERN's database, and for S;G 0 they put Kagari's memory back in her head. How exactly does this change the world line if the past is not touched at all?