Discount not applied

The discount is being applied on the item line in the cart, but the subtotal and total are not being calculated and applied. I have a custom function that seems to be interrupting it, but not sure why or where.

// add unpaid entries to cart
add_action( 'pre_get_posts', 'add_entries_to_cart' );

function add_entries_to_cart() {
	global $woocommerce;

	// Check we are logged in
	if ( is_user_logged_in() ) {

		// Check if we are in admin area
		if ( ! is_admin() ) {
			$user = wp_get_current_user();
			$entries = get_user_meta($user->ID, 'entry_count', true);
			$entries_paid = get_user_meta($user->ID, 'paid_entries', true);

			$product_id = 229;
			$quantity = $entries - $entries_paid;

			$found = false;
			//check if product already in cart, get id
			if ( sizeof( $woocommerce->cart->get_cart() ) > 0 ) {
				foreach ( $woocommerce->cart->get_cart() as $cart_item_key => $values ) {
					$_product = $values['data'];
					if ( $_product->id == $product_id ) {
						// correct quantity
						// Get it's unique ID within the Cart
						$prod_unique_id = $woocommerce->cart->generate_cart_id( $product_id );
						$woocommerce->cart->set_quantity( $prod_unique_id, $quantity );
						$found = true;
					}
				}
				// if product not found, add it
				if ( ! $found ) {
					$woocommerce->cart->add_to_cart( $product_id, $quantity );
				}
			}
			// no product in cart so add it
			else {
				// add to cart
				$woocommerce->cart->add_to_cart( $product_id, $quantity );
			}
		}
	}
}

It’s related to these two lines:

$prod_unique_id = $woocommerce->cart->generate_cart_id( $product_id );
$woocommerce->cart->set_quantity( $prod_unique_id, $quantity );

If I remove them it works, but people can change the quantity of items in their cart, which I don’t want.