I don't know which uninstaller did it, but many times after uninstalling scenery I noticed a lot of addons don't work right anymore, or completely crash when trying to load them, such as Reality XP avionics. The fix is to run the Flight1 registry entry program. But why does this happen? What makes an uninstaller remove the fsx registry location?

If using the clickteam installer, you can read the FSX directory from the registry (as shown in the attached screenshot from the installer program maker).

 

But, if you tick the Update Key tickbox then it will eff up the FSX registry. Unfortunately the tickbox is usually ticked by default so many people creating their own installers make this mistake.