How to retrieve php files?

Hello, Over the past few weeks our site has been experiencing red site blocks from google about malicious content, however, when I check the file manager in blue host- there is nothing recently modified. I have no time to work on the site so my mom (who owns the site) took it upon herself to fix it. Using wordfence plugin, she removed anything that had a warning of malicious content (even though there wasn't) and in doing so, she removed the header and possibly other important elements that make up the site. Now our site has no header or menu. How do I get it back? http://www.stoneagect.com Many Thanks, Mandala528