You can not install other version of installed plugin via .zip file. You have to delete plugin via WordPress before install it this way as you will always get “Destination folder already exists” error message. Deleting plugin via WordPress will delete the settings you made for URE. So its better to deactivate plugin and remove its folder via FTP or file manager.
If you input a license key at the “Settings->User Role Editor->General” tab, it will be possible to update URE Pro directly from WordPress as any other plugin – from the Plugins or Updates pages. License key is available at your account page after login. Read this article for more details.