Ah, I understand now. Thanks for explaining tili.
A lot of exposure to ongoing fiction has given me a different view, I suppose. I agree that each work should stand on it's own and contain everything needed for the story to be understood, but expanding on past stories by adding new details is very common in some mediums. My opinion is that the story always belongs to the author, even after it is released. If the author wants to go back and reveal a new detail or expand on a story, they have that right. Sometimes it does backfire on them and result in fan uproar, so it should not be done lightly. George Lucas has taken a lot of flak for making changes in Star Wars, but ultimately those were his stories to tell. At other times, fans embrace changes like this as a way to tell new stories.
Of course, I'm also conditioned to sometimes think of "the author" as a corporation rather than an individual. Like for Phantasy Star, I think of the story author as Sega and not Ozaki, Kodama or the other individuals who worked on the games. Sega is the one with the ultimate authority to choose what is or isn't canon to the story. Ozaki wouldn't have the authority to say a particular branch of PSIII is more canon than another, unless Sega made a game that said the same thing first. Likewise I wouldn't consider Chaz's son canon, that's just fun speculation on what might have happened later.
Reviving Nei is a bad example for your point, though. Sega has already done that twice, in the Drama CD and Generation:2. Neither changed the value of the original PSII story. The original is always still there and can be considered on its own merits.