Q25: In 999, Akane disappears when you don’t reach the True Ending. This implies that changing the past affects the present.
     In VLR, Tenmyouji explains to “?” at the end that even if Sigma could change the past, the timeline that they live in will remain the same.
     If Sigma can stop Radical-6 in the past, this will only create a new timeline. This implies that changing the past does NOT affect the present. Don’t these games have contradicting ideas?

     Even if you had changed the past and prevented Radical-6 from spreading, the setting is made so that there will be no changes made to the VLR history.
     And let’s say VLR’s history does get destroyed. Then Sigma’s old consciousness won’t be able to return to 2028 and as a result he won’t be able to stop the Radical-6 outbreak.
Same goes for 999. The true end is where Junpei accesses the Morphogenetic Field 9 years ago and saves Akane, but if he isn’t successful, then a new timeline is created. And the extension of that history is the Junpei who couldn’t find Akane at the chapel. (*We call this end that isn’t the True End the B End.)
     However, there may be some of you that will say “Hey, Akane did exist in the B End route though”. Well you’re exactly right. In that history Akane should not have existed.
     So in other words, the contradiction isn’t the setting between 999 and VLR, but rather it is in the B Ending. However, if you consider that Akane had jumped to the B End route with her whole body and not just her psyche then it would all make sense…
     If that is the case, then Akane did not disappear in the chapel but she just made her escape, or you can say that her whole body jumped to another time line.