I repeated a problem at my test environment emulating fake data from AD.
Code after which user loses his URE created meta data is ad-integration.php, line #2784:

if ($display_name != '') {
	wp_update_user(array('ID' => $user_id, 'display_name' => $display_name));

But it is correct. It just shows the bug in my own code, where I delete metadata if there is empty value of a correspondent POST array element, like this:

if (!empty($_POST['ure_posts_list'])) {
} else {
  delete_user_meta($user_id, $this->umk_posts_list);

This code is definitely fired when user profile is updated not from the web-page but via WordPress API call. So I confirm the bug in User Role Editor Pro and will develop a fix for it.

Thanks a lot for your help in discovering this issue. Update will be available in a week.