I need to deploy everything but users. I noticed that when I deploy applications using the Console, if the shared role names have been updated in the source repository, they are not updated in the destination repository. However, if I deploy the entire repository, the shared roles are updated but users are also copied. How can I copy EVERYTHING but the users?

To do this, select the option "Deploy an application" instead of "Deploy the Repository".
When you use "Deploy an application" with "always overwrite an existing application" and "Refresh", Visual Guard .Net refreshes your target application in your VG Repository target.