1. Did Akane die 9 years ago, and if so, how is she alive now? It makes sense for her to be alive, but that leads to question 2: If Akane lived, were Snake, Seven and Clover lying about her death? The answers give semi-contradictory/ambiguous remakrs regarding these questions. They give this whole blurb about Akane having died both don't give a good explanation of how she was alive in the present, THEN go on to say Seven (and Snake? I forget if they list him) were lying, indicating Akane lived, which they just said she didn't!
But I'm OK with leaving those two points up for debate. I think they give enough support in-game for both sides of those theories to be true. And all great stories leave some interpretation up to the reader. That being said, I like to think that Akane lived, and Snake/Clover/Seven were implanted false memories by Akane using the Morphogenetic field.