RadarMan is right it's not so easy and it's the dll's. It says much of this right on the Microsoft website. Mentions something about 'if you don't feel comfortable ' with dll or blank or blank (whatever the case is there as it is listed) re-creating files etc. It's best to forego the update even though it is a cool one. I believe the update you are talking about is mainly the bridges etc?
Having said that about the cautionary verbiage, I guess it is a forgone conclusion that what is now done is done. I am sure that there are folks aboard here on Fly Away like Radar that can assist you in some way lest you have to do the most dreaded uninstall.
The Microsoft website also has some guidelines on the FS9 home page.
http://www.microsoft.com/games/flightsimulator/support.asp
Good luck with it and I hope all works out well with this issue.