I am having an issue with updating Toolset plugins with Installer. I have installed the Installer and then followed your solution (https://toolset.com/forums/topic/installer-not-working-wp-4-0/) by changing the endpoint URL to hidden link. Now I can login, which was not possible before, however it does not allow me update the plugins (error says "Destination folder already exists".) ?
Also, can you please confirm (since the menu options are a bit confusing) when I "install" the plugin that has already been installed it will not overwrite what I've already got and I won't loose the my work (I would have expected to see an "update" option in the menu)
With installer you can only update plugins that were installed with him.
The message that you are getting is because the plugin you are trying to update is already installed and was not by Installer.
So my suggestion would be to change the name of the plugin directory that you want to update ( this will allow for easy rollback if necessary ). Then run the installer for the plugin in question in this case it will install as new.
The database data that you currently have in your site relative to the plugin is not affected by this. For example if you are updating Types, any custom post type previously create will not be deleted by the update of the plugin.