diff --git a/mod/assign/db/upgrade.php b/mod/assign/db/upgrade.php
index ade4b79021b..300f574d4ed 100644
--- a/mod/assign/db/upgrade.php
+++ b/mod/assign/db/upgrade.php
@@ -584,5 +584,37 @@ function xmldb_assign_upgrade($oldversion) {
     // Moodle v2.8.0 release upgrade line.
     // Put any upgrade step following this.
 
+    if ($oldversion < 2014122600) {
+        // Delete any entries from the assign_user_flags and assign_user_mapping that are no longer required.
+        if ($DB->get_dbfamily() === 'mysql') {
+            $sql1 = "DELETE {assign_user_flags}
+                       FROM {assign_user_flags}
+                  LEFT JOIN {assign}
+                         ON {assign_user_flags}.assignment = {assign}.id
+                      WHERE {assign}.id IS NULL";
+
+            $sql2 = "DELETE {assign_user_mapping}
+                       FROM {assign_user_mapping}
+                  LEFT JOIN {assign}
+                         ON {assign_user_mapping}.assignment = {assign}.id
+                      WHERE {assign}.id IS NULL";
+        } else {
+            $sql1 = "DELETE FROM {assign_user_flags}
+                WHERE NOT EXISTS (
+                          SELECT 'x' FROM {assign}
+                           WHERE {assign_user_flags}.assignment = {assign}.id)";
+
+            $sql2 = "DELETE FROM {assign_user_mapping}
+                WHERE NOT EXISTS (
+                          SELECT 'x' FROM {assign}
+                           WHERE {assign_user_mapping}.assignment = {assign}.id)";
+        }
+
+        $DB->execute($sql1);
+        $DB->execute($sql2);
+
+        upgrade_mod_savepoint(true, 2014122600, 'assign');
+    }
+
     return true;
 }
diff --git a/mod/assign/locallib.php b/mod/assign/locallib.php
index 4c960b9f090..a6666b1bb72 100644
--- a/mod/assign/locallib.php
+++ b/mod/assign/locallib.php
@@ -700,9 +700,11 @@ class assign {
         }
 
         // Delete_records will throw an exception if it fails - so no need for error checking here.
-        $DB->delete_records('assign_submission', array('assignment'=>$this->get_instance()->id));
-        $DB->delete_records('assign_grades', array('assignment'=>$this->get_instance()->id));
-        $DB->delete_records('assign_plugin_config', array('assignment'=>$this->get_instance()->id));
+        $DB->delete_records('assign_submission', array('assignment' => $this->get_instance()->id));
+        $DB->delete_records('assign_grades', array('assignment' => $this->get_instance()->id));
+        $DB->delete_records('assign_plugin_config', array('assignment' => $this->get_instance()->id));
+        $DB->delete_records('assign_user_flags', array('assignment' => $this->get_instance()->id));
+        $DB->delete_records('assign_user_mapping', array('assignment' => $this->get_instance()->id));
 
         // Delete items from the gradebook.
         if (! $this->delete_grades()) {
@@ -761,19 +763,18 @@ class assign {
                 }
             }
 
-            $assignssql = 'SELECT a.id
-                             FROM {assign} a
-                           WHERE a.course=:course';
-            $params = array('course'=>$data->courseid);
+            $assignids = $DB->get_records('assign', array('course' => $data->courseid), '', 'id');
+            list($sql, $params) = $DB->get_in_or_equal(array_keys($assignids));
 
-            $DB->delete_records_select('assign_submission', "assignment IN ($assignssql)", $params);
+            $DB->delete_records_select('assign_submission', "assignment $sql", $params);
+            $DB->delete_records_select('assign_user_flags', "assignment $sql", $params);
 
             $status[] = array('component'=>$componentstr,
                               'item'=>get_string('deleteallsubmissions', 'assign'),
                               'error'=>false);
 
             if (!empty($data->reset_gradebook_grades)) {
-                $DB->delete_records_select('assign_grades', "assignment IN ($assignssql)", $params);
+                $DB->delete_records_select('assign_grades', "assignment $sql", $params);
                 // Remove all grades from gradebook.
                 require_once($CFG->dirroot.'/mod/assign/lib.php');
                 assign_reset_gradebook($data->courseid);
diff --git a/mod/assign/version.php b/mod/assign/version.php
index fd7b5c5c3fb..96d2675fef4 100644
--- a/mod/assign/version.php
+++ b/mod/assign/version.php
@@ -25,8 +25,6 @@
 defined('MOODLE_INTERNAL') || die();
 
 $plugin->component = 'mod_assign'; // Full name of the plugin (used for diagnostics).
-$plugin->version  = 2014111000;    // The current module version (Date: YYYYMMDDXX).
+$plugin->version  = 2014122600;    // The current module version (Date: YYYYMMDDXX).
 $plugin->requires = 2014110400;    // Requires this Moodle version.
 $plugin->cron     = 60;
-
-