Using functions.php to load header/footer

I developed a site using the Goran theme before I found out that it was already a child of Edin and I therefore can’t make another child. All my style editing is done in customised CSS so that’s fine when updates are made. However, the two files I edited in the theme itself (I know, I know!) are header.php and footer.php and these changes are obviously lost when updates are made.

My question is, can I get around this by modifying the parent file functions.php and adding code to NOT update header/footer. Or can I ask it to load custom files header2.php and footer2.php (which I would copy from the originals)? What would the code be for this? (Note – the changes I have made are vastly different from the originals so it’s not just a case of specifying a different image or changing footer wording.)

I’m really hoping there’s a solution other than manually uploading header.php and footer.php every time an update is made 🙁