You don't show us at all how your cookie is constructed, so how do you think we can help you?.

My advice is to store the cart items in the session on the server side, and not in the client cookie. From Javascript, just reload the part of the cart page after removing an item.

Upon looking further at the fragments of your code, it seems you never store the items on the client but only store the items in the session already. So from your Javascript, you will need to send a request to your Perl code to remove an item. I recommend doing that without Javascript first and later add something like the jQuery .load() function to reload parts of an HTML page.