diff --git a/repository/lib.php b/repository/lib.php
index bb3c9a547d0..2a6fc41cc37 100644
--- a/repository/lib.php
+++ b/repository/lib.php
@@ -2416,9 +2416,10 @@ abstract class repository {
         $user_context = context_user::instance($USER->id);
         if ($file = $fs->get_file($user_context->id, 'user', 'draft', $itemid, $filepath, $filename)) {
             if ($tempfile = $fs->get_file($user_context->id, 'user', 'draft', $itemid, $newfilepath, $newfilename)) {
+                // Remember original file source field.
+                $source = @unserialize($file->get_source());
                 if ($tempfile->is_external_file()) {
                     // New file is a reference. Check that existing file does not have any other files referencing to it
-                    $source = @unserialize($file->get_source());
                     if (isset($source->original) && $fs->search_references_count($source->original)) {
                         return (object)array('error' => get_string('errordoublereference', 'repository'));
                     }
@@ -2427,6 +2428,14 @@ abstract class repository {
                 $file->delete();
                 // create new file
                 $newfile = $fs->create_file_from_storedfile(array('filepath'=>$filepath, 'filename'=>$filename), $tempfile);
+                // Preserve original file location (stored in source field) for handling references
+                if (isset($source->original)) {
+                    if (!($newfilesource = @unserialize($newfile->get_source()))) {
+                        $newfilesource = new stdClass();
+                    }
+                    $newfilesource->original = $source->original;
+                    $newfile->set_source(serialize($newfilesource));
+                }
                 // remove temp file
                 $tempfile->delete();
                 return true;
diff --git a/repository/upload/lib.php b/repository/upload/lib.php
index 47ad7a4be26..dbec79d3a6d 100644
--- a/repository/upload/lib.php
+++ b/repository/upload/lib.php
@@ -201,13 +201,14 @@ class repository_upload extends repository {
         $record->userid    = $USER->id;
 
         if (repository::draftfile_exists($record->itemid, $record->filepath, $record->filename)) {
+            $existingfilename = $record->filename;
+            $unused_filename = repository::get_unused_filename($record->itemid, $record->filepath, $record->filename);
+            $record->filename = $unused_filename;
+            $stored_file = $fs->create_file_from_pathname($record, $_FILES[$elname]['tmp_name']);
             if ($overwriteexisting) {
-                repository::delete_tempfile_from_draft($record->itemid, $record->filepath, $record->filename);
+                repository::overwrite_existing_draftfile($record->itemid, $record->filepath, $existingfilename, $record->filepath, $record->filename);
+                $record->filename = $existingfilename;
             } else {
-                $existingfilename = $record->filename;
-                $unused_filename = repository::get_unused_filename($record->itemid, $record->filepath, $record->filename);
-                $record->filename = $unused_filename;
-                $stored_file = $fs->create_file_from_pathname($record, $_FILES[$elname]['tmp_name']);
                 $event = array();
                 $event['event'] = 'fileexists';
                 $event['newfile'] = new stdClass;
@@ -221,10 +222,10 @@ class repository_upload extends repository {
                 $event['existingfile']->url      = moodle_url::make_draftfile_url($record->itemid, $record->filepath, $existingfilename)->out(false);
                 return $event;
             }
+        } else {
+            $stored_file = $fs->create_file_from_pathname($record, $_FILES[$elname]['tmp_name']);
         }
 
-        $stored_file = $fs->create_file_from_pathname($record, $_FILES[$elname]['tmp_name']);
-
         return array(
             'url'=>moodle_url::make_draftfile_url($record->itemid, $record->filepath, $record->filename)->out(false),
             'id'=>$record->itemid,