Source: IVAO Community Forum – Germany at http://de.forum.ivao.aero/index.php/topic,10197.0.html
By Kenny – http://www.ivao.aero/members/person/details.asp?id=108442

Flight Simulator – FS2004

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IV. QUICK FS REINSTALL PROCEDURE


Backup of your Settings
Make a backup of the following folder:
C:\Documents and Settings\<your user name>\Application Data\Microsoft\FS9

Restore the backup after doing the quick reinstall as described in the next point.

Backup of your FS System (Planes, Modules, Scenery,…)
Given you current install is in
C:\Program Files\Microsoft Games\Flight Simulator 9
(if not, addapt further references to this path a bit)

Rename this directory to
C:\Program Files\Microsoft Games\Flight Simulator 9 Backup

Now do a minimal install, in the original directory
C:\Program Files\Microsoft Games\Flight Simulator 9

Apply the update 9.1 patch (only if you did it before too)

To finish, delete the
C:\Program Files\Microsoft Games\Flight Simulator 9

Rename the
C:\Program Files\Microsoft Games\Flight Simulator 9 Backup
back to
C:\Program Files\Microsoft Games\Flight Simulator 9