Index: lams_central/src/java/org/lamsfoundation/lams/webservice/SPEnrolmentServlet.java
===================================================================
diff -u -r657c3ddcb79ba8772e462cc797d2937dd88292cc -rf6a638aaf02124adf0a3a519440b3b31496937ae
--- lams_central/src/java/org/lamsfoundation/lams/webservice/SPEnrolmentServlet.java	(.../SPEnrolmentServlet.java)	(revision 657c3ddcb79ba8772e462cc797d2937dd88292cc)
+++ lams_central/src/java/org/lamsfoundation/lams/webservice/SPEnrolmentServlet.java	(.../SPEnrolmentServlet.java)	(revision f6a638aaf02124adf0a3a519440b3b31496937ae)
@@ -332,10 +332,8 @@
 		// users who are part of courses but are not in the file anymore are eligible for disabling
 		allExistingUsersFromParsedCourses.removeAll(allParsedUsers);
 		for (User user : allExistingUsersFromParsedCourses) {
-		    // make a flat set of roles from all subcourses
-		    Set<Integer> roles = userManagementService.getRolesForUser(user.getUserId()).values().stream()
-			    .collect(HashSet::new, Set::addAll, Set::addAll);
-		    if (roles.isEmpty()) {
+		    boolean hasAnyRoles = userManagementService.hasUserAnyRoles(user.getUserId());
+		    if (!hasAnyRoles) {
 			// he is only a learner or this is staff mode, so disable
 			userManagementService.disableUser(user.getUserId());
 
Index: lams_common/src/java/org/lamsfoundation/lams/usermanagement/service/IUserManagementService.java
===================================================================
diff -u -r346836ed4a3680af233482b184e7371ec5b620bc -rf6a638aaf02124adf0a3a519440b3b31496937ae
--- lams_common/src/java/org/lamsfoundation/lams/usermanagement/service/IUserManagementService.java	(.../IUserManagementService.java)	(revision 346836ed4a3680af233482b184e7371ec5b620bc)
+++ lams_common/src/java/org/lamsfoundation/lams/usermanagement/service/IUserManagementService.java	(.../IUserManagementService.java)	(revision f6a638aaf02124adf0a3a519440b3b31496937ae)
@@ -246,6 +246,11 @@
     Map<Integer, Set<Integer>> getRolesForUser(Integer userId);
 
     /**
+     * Checks if given user has got any roles in any organisation.
+     */
+    boolean hasUserAnyRoles(Integer userId);
+
+    /**
      * @param login
      * @param typeId
      * @param stateId
Index: lams_common/src/java/org/lamsfoundation/lams/usermanagement/service/UserManagementService.java
===================================================================
diff -u -r3080c61fc08c0d5fdc28fb9ad6c8ab51363693d9 -rf6a638aaf02124adf0a3a519440b3b31496937ae
--- lams_common/src/java/org/lamsfoundation/lams/usermanagement/service/UserManagementService.java	(.../UserManagementService.java)	(revision 3080c61fc08c0d5fdc28fb9ad6c8ab51363693d9)
+++ lams_common/src/java/org/lamsfoundation/lams/usermanagement/service/UserManagementService.java	(.../UserManagementService.java)	(revision f6a638aaf02124adf0a3a519440b3b31496937ae)
@@ -402,7 +402,17 @@
 	return baseDAO.findByProperties(UserOrganisation.class, properties);
     }
 
+    /**
+     * Checks if given user has got any roles in any organisation.
+     */
     @Override
+    public boolean hasUserAnyRoles(Integer userId) {
+	Map<String, Object> properties = new HashMap<>();
+	properties.put("userOrganisation.user.userId", userId);
+	return baseDAO.countByProperties(UserOrganisationRole.class, properties) > 0;
+    }
+
+    @Override
     public List getUserOrganisationsForUserByTypeAndStatusAndParent(String login, Integer typeId, Integer stateId,
 	    Integer parentOrgId) {
 	Map<String, Object> properties = new HashMap<>();