diff --git a/course/edit.php b/course/edit.php
index f257f910018..b88ab774f76 100644
--- a/course/edit.php
+++ b/course/edit.php
@@ -45,8 +45,11 @@ if ($id) {
         print_error('cannoteditsiteform');
     }
 
-    $course = course_get_format($id)->get_course();
+    // Login to the course and retrieve also all fields defined by course format.
+    $course = get_course($id);
     require_login($course);
+    $course = course_get_format($course)->get_course();
+
     $category = $DB->get_record('course_categories', array('id'=>$course->category), '*', MUST_EXIST);
     $coursecontext = context_course::instance($course->id);
     require_capability('moodle/course:update', $coursecontext);
diff --git a/course/format/lib.php b/course/format/lib.php
index 38c4a69b989..a68ce5ae500 100644
--- a/course/format/lib.php
+++ b/course/format/lib.php
@@ -237,14 +237,21 @@ abstract class format_base {
         if ($this->course === false) {
             $this->course = get_course($this->courseid);
             $options = $this->get_format_options();
+            $dbcoursecolumns = null;
             foreach ($options as $optionname => $optionvalue) {
-                if (!isset($this->course->$optionname)) {
-                    $this->course->$optionname = $optionvalue;
-                } else {
-                    debugging('The option name '.$optionname.' in course format '.$this->format.
-                        ' is invalid because the field with the same name exists in {course} table',
-                        DEBUG_DEVELOPER);
+                if (isset($this->course->$optionname)) {
+                    // Course format options must not have the same names as existing columns in db table "course".
+                    if (!isset($dbcoursecolumns)) {
+                        $dbcoursecolumns = $DB->get_columns('course');
+                    }
+                    if (isset($dbcoursecolumns[$optionname])) {
+                        debugging('The option name '.$optionname.' in course format '.$this->format.
+                            ' is invalid because the field with the same name exists in {course} table',
+                            DEBUG_DEVELOPER);
+                        continue;
+                    }
                 }
+                $this->course->$optionname = $optionvalue;
             }
         }
         return $this->course;
diff --git a/lib/db/upgrade.php b/lib/db/upgrade.php
index 0fe0e436348..6aff33e5cb6 100644
--- a/lib/db/upgrade.php
+++ b/lib/db/upgrade.php
@@ -85,7 +85,7 @@ defined('MOODLE_INTERNAL') || die();
  * @return bool always true
  */
 function xmldb_main_upgrade($oldversion) {
-    global $CFG, $USER, $DB, $OUTPUT, $SITE;
+    global $CFG, $USER, $DB, $OUTPUT, $SITE, $COURSE;
 
     require_once($CFG->libdir.'/db/upgradelib.php'); // Core Upgrade-related functions
 
@@ -316,6 +316,10 @@ function xmldb_main_upgrade($oldversion) {
             $dbman->drop_field($table, $field);
         }
 
+        // Since structure of 'course' table has changed we need to re-read $SITE from DB.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         upgrade_main_savepoint(true, 2012031500.02);
     }
 
@@ -447,6 +451,10 @@ function xmldb_main_upgrade($oldversion) {
             $dbman->add_field($table, $field);
         }
 
+        // Since structure of 'course' table has changed we need to re-read $SITE from DB.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         // Main savepoint reached
         upgrade_main_savepoint(true, 2012050300.03);
     }
@@ -563,6 +571,10 @@ function xmldb_main_upgrade($oldversion) {
             $dbman->add_field($table, $field);
         }
 
+        // Since structure of 'course' table has changed we need to re-read $SITE from DB.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         // Add course_sections_availability to add completion & grade availability conditions
         $table = new xmldb_table('course_sections_availability');
 
@@ -1334,6 +1346,10 @@ function xmldb_main_upgrade($oldversion) {
         // Launch change of type for field format
         $dbman->change_field_type($table, $field);
 
+        // Since structure of 'course' table has changed we need to re-read $SITE from DB.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         // Main savepoint reached
         upgrade_main_savepoint(true, 2012110200.00);
     }
@@ -1386,6 +1402,10 @@ function xmldb_main_upgrade($oldversion) {
             }
         }
 
+        // Since structure of 'course' table has changed we need to re-read $SITE from DB.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         // Main savepoint reached
         upgrade_main_savepoint(true, 2012110201.00);
     }
@@ -1501,6 +1521,7 @@ function xmldb_main_upgrade($oldversion) {
         if ($SITE->format !== 'site') {
             $DB->set_field('course', 'format', 'site', array('id' => $SITE->id));
             $SITE->format = 'site';
+            $COURSE->format = 'site';
         }
 
         // Main savepoint reached
@@ -1989,6 +2010,10 @@ function xmldb_main_upgrade($oldversion) {
             $dbman->drop_field($table, $field);
         }
 
+        // Since structure of 'course' table has changed we need to re-read $SITE from DB.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         // Main savepoint reached.
         upgrade_main_savepoint(true, 2013040300.01);
     }
@@ -2376,6 +2401,10 @@ function xmldb_main_upgrade($oldversion) {
             $dbman->add_field($table, $field);
         }
 
+        // Since structure of 'course' table has changed we need to re-read $SITE from DB.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         // Define field calendartype to be added to user.
         $table = new xmldb_table('user');
         $field = new xmldb_field('calendartype', XMLDB_TYPE_CHAR, '30', null, XMLDB_NOTNULL, null, 'gregorian');
@@ -2400,6 +2429,10 @@ function xmldb_main_upgrade($oldversion) {
             $dbman->add_field($table, $field);
         }
 
+        // Since structure of 'course' table has changed we need to re-read $SITE from DB.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         // Main savepoint reached.
         upgrade_main_savepoint(true, 2013091000.02);
     }
@@ -2423,6 +2456,10 @@ function xmldb_main_upgrade($oldversion) {
             $dbman->drop_field($table, $field);
         }
 
+        // Since structure of 'course' table has changed we need to re-read $SITE from DB.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         // Main savepoint reached.
         upgrade_main_savepoint(true, 2013091000.03);
     }
diff --git a/lib/upgradelib.php b/lib/upgradelib.php
index 338a5ccf804..472b32a5ab1 100644
--- a/lib/upgradelib.php
+++ b/lib/upgradelib.php
@@ -1503,7 +1503,7 @@ function install_core($version, $verbose) {
  * @return void, may throw exception
  */
 function upgrade_core($version, $verbose) {
-    global $CFG;
+    global $CFG, $SITE, $DB, $COURSE;
 
     raise_memory_limit(MEMORY_EXTRA);
 
@@ -1534,6 +1534,10 @@ function upgrade_core($version, $verbose) {
             upgrade_main_savepoint($result, $version, false);
         }
 
+        // In case structure of 'course' table has been changed and we forgot to update $SITE, re-read it from db.
+        $SITE = $DB->get_record('course', array('id' => $SITE->id));
+        $COURSE = clone($SITE);
+
         // perform all other component upgrade routines
         update_capabilities('moodle');
         log_update_descriptions('moodle');