Yes, you may update it manually. You will not lose any piece of data unless you do not click ‘Delete’ link at the “Plugins” page. If you delete current version of the plugin via WordPress you will lose the settings you made.
Steps for the safe plugin version update:
1) Deactivate URE Pro.
2) Delete ‘user-role-editor-pro’ folder via FTP.
3) extract the latest version to wp-content/plugins from the Pro version .zip file you downloaded from role-editor.com
4) activate plugin back.
I may to guess only why current permissions to URE Pro folders and files differs from others.
Do you have SSH (command line via terminal window) access to your WordPress server file system? Is it possible for you to show me the output of some commands related to the file permissions management? I mean to check the current permissions, compare them with other plugin folder and set them the same way.