First of all, it would be $modx->user->removeSessionCookie(), but you do not need to end the session or remove the cookie (and that function does nothing currently). You simply need to refresh the appropriate user session data.
If all you want to do is reload user access permissions for web, you can:
<?php
$modx->user->loadAttributes(array(), 'web', true);
?>
However, I think the API functions modUser::joinGroup() and modUser::leaveGroup() should call this automatically, as well as remove any other stale session data related to user access permissions (Resource Groups, User Groups, etc.). I’ll add a ticket to make this happen. In the meantime, if you want to refresh this other data manually, you can unset any $_SESSION data with the key
modx.user.{id}. (where {id} is the $modx->user->id), e.g.
<?php
$key = "modx.user.{$modx->user->id}";
$keyLength = strlen($key);
foreach ($_SESSION as $sKey => $sVal) {
if (substr($sKey, 0, $keyLength) === $key) unset($_SESSION[$sKey]);
}
?>
I assume you are using modUser::joinGroup() and/or modUser::leaveGroup() API functions to modify their memberships?