Mirikon:
Thank you for the suggestion. Yes, I can do as you suggest, and say the invalidated plotline was a ruse of some kind. but what you are offering me is techniques for correcting the damage that my campaign wouldn't have suffered in the first place if the game writers had know what was actually going on in the game universe and then shared a significant part of it with me. When I buy a sourcebook, I expect there to be canon material in it - not material that might or might not be canon.
I beg your patience with the frostiness my tone now takes on in replying to your suggestion that I am not "exercising enough creativity". I was a Shadowrun gamemaster when you were six years old. To quote Roy Batty, I have seen things you people wouldn't believe. Lack of creativity is not the problem.
It's not 'damage'. I think your trying far to hard to adhere to the material in the book, when the material itself is open to interpretation, internal consistency is never going to perfect, and thus things either get 'dropped' or gains greater value then originally presented.
But to expect that to be clear? is unreasonable. Writers create as they go, and while most have an idea where they are going, they can change direction due to a piece they wrote (for example, they like the minor character they created and move him into main character status). Now, when your talking about Shadowrun with 20+ years of published material and a number of writers etc, there is no way you can reasonable expect the material not to change
And that's ignoring the writers perogative to have plot twists. eg Lowfry and Hestaby situation is got to be far more complicated that what it appears. But we will have to wait and find out... and maybe the writers will tell us one day, or maybe not?
So either you wait until the Shadowrun line is dropped (and thus you have freedom from metaplot changes), play against the metaplot of an earlier edition (cause at least then you 'know' what's coming), or... heck if I know? Ignore all source material? Make a 'hourse rule' which says your campaign is canon and source material is suggestion. (Actually, I think a lot of people do play this way. Why the heck not?) Um.. play away from source material? Therefor metaplot events happen 'elsewhere', and can be ignored?
Stop treating the campaign books like they 'must be obeyed!'. It takes the fun out of the game. Just enjoy them for what they are, good fiction which should enhance your game, not detract. Either work with or don't. It should not be a big issue.
Now, my final issue, your response to Mirikon. I think his suggestIon was a valid. His not having issues with source material. You are. Despite playing for x number of years. Fact: "Correlation does not imply causation". Age does not equal experience. Also, you imply that Mirikon and others don't have your 'experience' thus their valid suggestions are not valid and this is very disrespectful. So what you hope to get by posting here is beyond me.