The sync_reference function in repository/filesystem/lib.php has this code:

if (file_extension_in_typegroup($filepath, 'web_image')) {
$contenthash = sha1_file($filepath);
if ($file->get_contenthash() == $contenthash)

{ // File did not change since the last synchronisation. $filesize = filesize($filepath); }

else

{ // Copy file into moodle filepool (used to generate an image thumbnail). list($contenthash, $filesize, $newfile) = $fs->add_file_to_pool($filepath); }

} else

{ // Update only file size so file will NOT be copied into moodle filepool. $contenthash = null; $filesize = filesize($filepath); }

The first if clause is preventing any alias file, that is not an image, to be able to be synchronized with its source file stored in a file system repository when calling to $file->sync_external_file();