If it is a full on retcon, then I would hope they include all of the A3, and AR material in the book somehow in the 2nd edition. But it would be difficult to maintain the "WY files" vibe to it if we are posed with alternate time lines...
Given Blomkamp's statements, I reckon it is.
Thing is with source books, they usually are printed long before a new installment is arrived. Like the Marvel Handbook Guides, they are printed before certain events are published, and when retcons happen.. more or less they are treated as authorative until the retcon takes place. So really... I see that happening here.
This will be authorative... until Blomkamp's sequel comes out and re-assigns Alien 3 and Resurrection.