I have never been in that directory, no reason to go there until today looking to replace sound file with new AVSIM flile so I could not have removed it.
Whole folders don't disappear by themselves and since (according to your description) everything else works, which obviously safely discount the fact you haven't installed GSX, it can only due to "something" in your system that have removed it, whether you did intentionally or not, or you had some kind of unusual system problem, like a corrupted hard disk sector, it's not really relevant but, you can be sure the folder should be there, because the installer will always put it there.
I want to reinstall GSX how would I do it I want to be sure I do not disturb Couatl
Why you think it should "disturb" it ?? Nothing in our installation will obviously disturb our own stuff, when there are problems, they are ALWAYS caused by other products (usually antivirus) or other problems in your system (like missing system libraries) but, if you have correctly configured the antivirus and finally fixed any system problems that prevented the program to run before, there's no reason uninstalling/reinstalling would cause any problem.
Do I do this thru Virtuali using De-Activate and then Reinstall or do I have to remove thru Add Remove Programs. and download the product over again.
If there was any need to do anything special, I would obviously said to do that. As explained many times already and as clearly indicated everywhere on the manuals, on the forum and on the FAQ page, you will NEVER, EVER lose your registration or need to deactivate or reactivate if you JUST uninstall/reinstall.
The only time you need to deactivate and reactivate, is if you have to reinstall *WINDOWS* from scratch OR if you change a major hardware component. You can even remove your entirely FSX, the activation wouldn't be affected at all, since it's NOT stored in FSX, it's stored in your Windows registry. You can uninstall/reinstall the program an unlimited number of times, registration will never be affected.