We haven't said anything about uninstalling being required, so you can safely assume it's not required. And if it was, the installer would have checked for that.
None of your customizations are ever affected, not by reinstalling GSX (even if you uninstall it) of even by a complete reinstall of the simulator.
Generally speaking, the whole point of the %APPDATA% folder, for any Windows application, is to store your own stuff, so no Uninstaller is supposed to remove anything there, unless it comes with some specific option like asking to clear your preferences, but it should never be automatic, and we comply to this rule.
