I m storing cookies using javascript it's working good and I am getting the data on checkout page. In case of adding two products in the cart I can only see cookie data until the first product added into the cart, when the second product comes in I can only see previous cookies new cookies which are stored while adding second product are missing.
Instead of store cookies using javascript or PHP Try use
wc_setcookie("cookieName", "CookiValue", $expire = 0, $secure = false);