What happens when you put your FS2004 disc in the PC ? Does it autorun ?

I’d suggest a reinstall over the existing install (ie on the same location) and then try and remove it. Hopefully that should remove all trace of both installs
you may need to manually remove any files relating to add ons.

As an aside it’s highly unlikley that your flight sim installed has become corrupted on its own. You should always make changes to flight sim carefully and one at a time, it is easy to get carried away and even the most experianced users can get into difficulty.

Bruce