In my opinion, following the canon for Shadowrun isn't really that important. What makes Shadowrun is the style and environment. You have a standard cyberpunk dystopia with all the chaos of magic thrown in.
I've run games where every adventure was an official published one and the players oohed and awed over ever tasty morsel of the official storyline, but I've also run campaigns where the characters never made it out of the barrens and the players were still just as happy. If something doesn't jive for my campaign idea, I change it. The only thing I make sure to do is inform my players.
An example of this is my 2050 game that I run using SR4A. I retconned wireless in, but made it ineffective compared to a wired connection. So, every decker worth his salt uses a cyberdeck and jacks in, but I get to keep the niftyness that is AR. The matrix crash was just the wireless 1.0 crashing and wireless 2.0 was brought in to fix everything.
I believe that unless you're hopping to a different setting, you're still playing Shadowrun. After all, everyone has their own style.