did you try setting quantity to 0 ? I remember line items get deleted if you specify 0, something like:

order_contents = {
   order: { number: order.number,
      line_items_attributes: [{id: 1, quantity: 0}, {id: 2, quantity: 0}]
    }
post :orders_update_cart(token: user.spree_api_token). params: order_contents

makes sense, this works without a new endpoint, thanks!