Index: lams_common/src/java/org/lamsfoundation/lams/lesson/service/LessonService.java
===================================================================
diff -u -r6be225f8d21a7f927da78ca099fc8c3915d7668a -raf442b23ea96f0fb704ea3afddb41f1c778d4a01
--- lams_common/src/java/org/lamsfoundation/lams/lesson/service/LessonService.java	(.../LessonService.java)	(revision 6be225f8d21a7f927da78ca099fc8c3915d7668a)
+++ lams_common/src/java/org/lamsfoundation/lams/lesson/service/LessonService.java	(.../LessonService.java)	(revision af442b23ea96f0fb704ea3afddb41f1c778d4a01)
@@ -289,7 +289,6 @@
 	    if (grouper != null) {
 		try {
 		    grouper.removeAllLearnersFromGrouping(grouping);
-		    grouping.getGroups().clear();
 		} catch (GroupingException e) {
 		    throw new LessonServiceException(e);
 		}
@@ -358,7 +357,9 @@
 
 	    // nuke all existing groups and create new ones
 	    removeAllLearnersFromGrouping(grouping);
+	    grouping.getGroups().clear();
 	    groupingDAO.flush();
+
 	    for (OrganisationGroup orgGroup : orgGrouping.getGroups()) {
 		Group group = Group.createLearnerGroup(grouping, orgGroup.getName(),
 			new HashSet<>(orgGroup.getUsers()));
Index: lams_monitoring/src/java/org/lamsfoundation/lams/monitoring/web/GroupingUploadAJAXController.java
===================================================================
diff -u -re226c52b735351f433827ce6b4c040714f3e6046 -raf442b23ea96f0fb704ea3afddb41f1c778d4a01
--- lams_monitoring/src/java/org/lamsfoundation/lams/monitoring/web/GroupingUploadAJAXController.java	(.../GroupingUploadAJAXController.java)	(revision e226c52b735351f433827ce6b4c040714f3e6046)
+++ lams_monitoring/src/java/org/lamsfoundation/lams/monitoring/web/GroupingUploadAJAXController.java	(.../GroupingUploadAJAXController.java)	(revision af442b23ea96f0fb704ea3afddb41f1c778d4a01)
@@ -425,6 +425,17 @@
 
 	// remove all the existing users from their groups
 	lessonService.removeAllLearnersFromGrouping(grouping);
+	if (!grouping.isUsedForBranching()) {
+	    Iterator<Group> groupIterator = grouping.getGroups().iterator();
+	    while (groupIterator.hasNext()) {
+		Group group = groupIterator.next();
+		// remove empty groups
+		if (group.getUsers().isEmpty() && group.getBranchActivities().isEmpty()) {
+		    groupIterator.remove();
+		}
+	    }
+	    userManagementService.save(grouping);
+	}
 
 	// Now put in the new users groupings
 	for (Map.Entry<String, Set<String>> groupEntry : groups.entrySet()) {