That’s a bit of a late answer and I don’t know if @Jay ever sorted it out, but to anyone having the same issue, here’s how I fixed it.
Menu Pages
function my_admin_menu() {
add_menu_page(
'Page title',
'Menu title',
'manage_options',
'my_page',
null,
null,
99
);
add_submenu_page(
'my_page',
'Subpage 1 title',
'Subpage 1 menu title',
'manage_options',
'my_subpage_1',
null
);
add_submenu_page(
'my_page',
'Subpage 2 title',
'Subpage 2 menu title',
'manage_options',
'my_subpage_2',
null
);
}
add_action( 'admin_menu', 'my_admin_menu' ) );
function my_admin_head() {
remove_submenu_page( 'my_page', 'my_subpage_1' );
}
add_action( 'admin_head', 'my_admin_head' );
See the Codex for remove_submenu_page.