All I can suggest is to back up any directories with VSTs in, and whatever data they refer to. Then do the uninstallation, and check the plugin manager to verify that nothing has gone missing. (And if so, restore the relevant files.)
Sadly Sonar doesn't do a good job of keeping things in consistent places, and Windows doesn't enforce this either, so you'll end up with stuff strewn across Program Files, Program Data, Appdata/Roaming, My Documents... all you can do is try to familiarise yourself with where everything is before you proceed.