First bit-they die, of course.
I was thinking more like when you are popping around between nodes in the flowchart. So say you got to a 'to be continued' part and then had to return to a previous door to get more information...actually it's probably just that since those time lines are basically parallel ones happening simultaneously, they probably just share a consciousness and access their memories through the morphogenetic field or some such. Never mind.
Second-You know what they say, hindsight is 20/20. I'm still living by the idea that every clue in these games can and will come to the surface. Clear picture of ZE3 as a result? Nah.
That said, Akane's existence, Seven's memories, and Sigma's age all weren't written well. However, foreshadowing and poor writing don't correlate. All three of these were foreshadowed. They were just poorly thought through ideas. And I do feel we shouldn't expect a seamless game, else folks like us will be disappointed with the series, if not already. I've come to appreciate over the months the level of detail in these games to the point where I'm willing to forgive--not forget--the poorly conceived bits of the narrative.
Some of those I felt were just ideas that were taken in a different direction than originally intended. The problem there is that there wasn't a lot of wiggle room to twist them to fit the new narrative. It seems to be an issue a lot of stories that go from a stand-alone tale to a trilogy seem to have. As for Sigma's age, that could have been handled better. Actually, having Sigma find out immediately that he was suddenly an old man could have been an interesting plot point and wouldn't have required such a huge suspension of disbelief from the player.