Secure wordpress_logged_in cookie

The advantage of a filter is that you can change a value without modifying core WP files. The filter you list:

$secure_logged_in_cookie = apply_filters('secure_logged_in_cookie', false, $user_id, $secure);

Passes in three values. You just need to build a function that accepts those three values and returns true (or just returns true by default.

This function, for example, merely returns true for whatever value is passed in to that filter:

add_filter( 'secure_logged_in_cookie', '__return_true' );