If you decide to hard code it you could take this line:
<a href="' . zen_catalog_href_link(FILENAME_DEFAULT) . '">
and change it to
<a href="http://www.yourdomain.com">
Or for more upgradeability:
<a href="' . HTTP_SERVER . '">
A quick fix that will get you what you need for the time being.
The 'long route' would be to open the /admin/includes/functions/html_output.php file and look for lines 72-74. These are the actual sections of the function which add the "main_page=index.php" portion to the strings.
That code section looks like this:
$link .= 'index.php?main_page='. $page;
} else {
$link .= 'index.php?main_page='. $page . "&" . zen_output_string($parameters);
If you wanted to program it out you could check the page being used and if it is the Recover cart system, alter the link (to remove the portion you don't want) else leave as is (for other links).
As far as the function href link reference, it should still work ok and there are a number of mods that still use the reference. In fact that function is still used in all 1.3.9 versions (in a number of locations) so I although there might be a transition in the works it has not been implemented at the moment.