I have done more digging, and I am still unsure what is happening. On the table wp_usermeta, URE uses a meta_key of wp_ure_posts_list and wp_ure_categories_list, as well as a meta_key named wp_ure_posts_restriction_type. I have values set in all 3, and after I run the ADI bulk import, it deletes the records for wp_ure_posts_lists and wp_ure_categories_list, but it leaves wp_ure_posts_restriction_type set. The section of code in ADI I think is relevant is:
// create new users or update them
if (!$user OR (strtolower($user->user_login) != strtolower($username))) { // use strtolower!!!
$user_id = $this->_create_user($ad_username, $userinfo, $display_name, $user_role, '', true);
$added_users++;
} else {
$user_id = $this->_update_user($ad_username, $userinfo, $display_name, $user_role, '', true);
$updated_users++;
}