If your site is in production and already linked to a thousand other places, make a whole bunch of redirect files ending with .html, i.e.
<html>
<head>
<title>myfile.html; redirect to myfile.php</title>
<meta http-equiv="refresh" content="0;url=http://www.mysite.com/myfile.php">
</head>
<body>
</body>
</html>
Thus, if anyone tries to link to the HTML files, they will be invisibly redirected to the PHP files. Problem solved, methinks.
Btw, if you're making a site that uses PHP at all, I'd be inclined to name every single file .php in case you decide to alter any files at a later date and include functionality and features which you hadn't thought of while you were initially making the website. I've got loads of files that are basically HTML, but I'm planning to include PHP-assisted features once I find the time and gain the necessary experience, so I've just named all files .php