Does page.tpl.php get overwritten on updates? Does page.tpl.php get overwritten on Drupal updates or are edits safe because it's in the theme folder? For some reason the developer put the footer HTML in here instead of creating a block for it... why I don't know.
For an drupal core update, you transfert every files/ folder except the sites folder for drupal 7.

Because in this folder, you have the setting.php and all your modules (custom or contrib) and your theme.

For module update, you can use the drupal ui or transfert the module update in the sites/all/modules folder.

So normaly, your theme and your page.tpl.php cannot be overide by an drupal core update.