How was this setup in the basic version? Did you edit the theme directly and add the template tag? Those changes wouldn't be saved, you would have to reapply them to the premium version.
To get the changes to stick, don't hack the theme directly, you will lose the changes again if you update the theme. If you can, add the slideshow using the widget or shortcode, or see if the theme has a theme option for that spot that accepts a shortcode.
If it isn't possible to add the slideshow as a widget or content you will have to use the template tag, but try to do it in a way that doesn't edit the original header.php file. Check the theme's documentation to see if there are hooks, you should be able to add PHP to the header using a hook. The theme developer should have documentation on how to do this if it has hooks.
Otherwise if there aren't any hooks there, create a child theme, copy the header.php file into the child theme, and edit the file there. When you update the parent theme, the child theme will be unaffected and you'll keep your changes.