To remove a shared folder right-click the version and select 'Administration | Manage Shared Folders'.
Select the shared folder you want to remove and press the 'Remove' button. You will then be given the option to delete the folder from the version.
If you choose to delete the folder then a changeset will be created deleting the shared folder with all its files and folders. If you choose not to delete the folder then the shared folders and files will not be changed, but the link to the shared folder will be removed. So updating these files and folders will no longer update the linked shared folder.