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Having different file types in of URLs in your site doesn't affect SEO. It may confuse  you, and you may inadvertently link internally to pages that don't exist on your site, but there is no effect on SEO. There is a way to parse HTML files as if they were PHP pages--but nowadays I don't recommend that. If you do have HTML pages on your site, you may just want to leave them alone. But if you do think you need to change or update their functionality, then setting up a 301 Permanent Redirect from the old HTML page to a new .PHP page, for example, will do just fine. It should not have any effect on rankings.