Actually, you would need to change the header and footer Home links individually. They use Zen Cart's HTTP_SERVER and DIR_WS_CATALOG constants which you cannot alter without breaking the store. You can easily change the link code to use just HTTP_SERVER which will point to the base domain URL.
Edit /includes/templates/your_template/common/tpl_header.php and tpl_footer.php.
PHP Code:
<li><?php echo '<a href="' . HTTP_SERVER . DIR_WS_CATALOG . '">'; ?><?php echo HEADER_TITLE_CATALOG; ?></a></li>
PHP Code:
<li><?php echo '<a href="' . HTTP_SERVER . '">'; ?><?php echo HEADER_TITLE_MAIN_SITE; ?></a></li>
Then add a define to /includes/languages/your_template/english.php like
PHP Code:
define('HEADER_TITLE_MAIN_SITE', 'Main Home');
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