What I am trying to do is include an HTML file within a PHP system (not a problem) but that HTML file also needs to be usable on its own, for various reasons, so I need to know
Use DOMDocument to keep what you need rather than strip what you don't need (PHP >= 5.3.6)
$d = new DOMDocument;
$d->loadHTMLFile($fileLocation);
$body = $d->getElementsByTagName('body')->item(0);
// perform innerhtml on $body by enumerating child nodes
// and saving them individually
foreach ($body->childNodes as $childNode) {
echo $d->saveHTML($childNode);
}