Paul. Uninstalling FS9 will not remove your Addon Scenery folder or any 3rd party scenery installed in it. Unless you have a problem caused by 3rd party scenery there's no need for you to remove it manually during the reinstall. Your 3rd party scenery will then only need reactivating after you've reinstalled FS9. All you need to do is take a backup copy of Scenery.cfg before uninstalling FS9 & paste it back in after reinstall is complete. This will only take a matter of seconds.
PS. I've only uninstalled FS9 once in all the years it's been on this old PC. That was only to find out what would happen for future reference.
Ta Doug...
Things are becoming clearer...
Just done a Windows search for "scenery.cfg" which is located within the FS 2004 Main Folder, and a file that gets removed in an "un-install"!
That is the file which you recommends being saved in a safe location BEFORE un-installation!
I must remember to do that next time...

...!
Every now and again I reinstall my FS 2004 to tidy it up....
..a bit like Hoovering my carpet..now and again...

...!
Paul...
Win 8.1 64-bit. DX11. Advent Tower. Intel i7-3770 3.9 GHz 8-core. 8 GB System RAM. AMD Radeon HD 7700 1GB RAM. DVD ROM. 2 Terra Byte SATA Hard Drive. Philips 17" LCD Monitor. Saitek Cyborg X Fly-5 Joystick. ...and a Briggs and Stratton Petrol Lawn Mower.