refund.php

<?php

namespace Patboard\Plugin;

/**
 * Class Cli_Command
 *
 */
class Cli_Command extends \WP_CLI_Command {

	/**
	 * @var string
	 */
	private $reason = 'VAT correction';

	/**
	 * Create refund orders for given order id's.
	 *
	 * @param $args
	 * @param $assoc_args
	 *
	 * @throws \Exception
	 */
	function refund( $args, $assoc_args ) {
		$orders = $assoc_args['orders'];
		$orders = explode( ',', $orders );

		if ( isset( $assoc_args['reason'] ) ) {
			$this->reason = $assoc_args['reason'];
		}

		foreach ( $orders as $orderid ) {
			$refunded = $this->refund_order( $orderid );

			if ( is_wp_error( $refunded ) ) {
				echo $orderid . ': ' . $refunded->get_error_message();
			}
		}
	}

	/**
	 * @param $orderid
	 *
	 * @return \WC_Order_Refund|\WP_Error
	 * @throws \Exception
	 */
	private function refund_order( $orderid ) {
		$order = wc_get_order( $orderid );

		// If it's something else such as a WC_Order_Refund, we don't want that.
		if ( ! is_a( $order, 'WC_Order' ) ) {
			return new \WP_Error( 'wc-order', 'Provided ID is not a WC Order' );
		}

		if ( 'refunded' == $order->get_status() ) {
			return new \WP_Error( 'wc-order', 'Order has been already refunded' );
		}

		// Get Items
		$order_items = $order->get_items( array( 'line_item', 'fee', 'shipping' ) );

		// Refund Amount
		$refund_amount = 0;

		// Prepare line items which we are refunding
		$line_items = [];

		// Iterating through order shipping items

		if ( ! $order_items ) {
			return new \WP_Error( 'wc-order', 'This order has no items' );
		}
		foreach ( $order_items as $item_id => $item ) {
			$line_total = $item->get_total();
			$qty        = $item->get_quantity();
			$tax_data   = $item->get_total_tax();

			$refund_tax = 0;

			if ( ! empty( $tax_data ) ) {
				$refund_tax = wc_format_decimal( $tax_data );
			}

			$refund_amount          = wc_format_decimal( $refund_amount ) + wc_format_decimal( $line_total );
			$line_items[ $item_id ] = array(
				'qty'          => $qty,
				'refund_total' => wc_format_decimal( $line_total ),
				'refund_tax'   => $refund_tax
			);
		}

		$refund = wc_create_refund( array(
			'amount'         => $refund_amount,
			'reason'         => $this->reason,
			'order_id'       => $orderid,
			'line_items'     => $line_items,
			'refund_payment' => false,
		) );

		return $refund;
	}
}

\WP_CLI::add_command( 'refund', array( __namespace__ . '\Cli_Command', 'refund' ) );

@pixelstart
I believe that's given in
$tax_data = wc_get_order_item_meta( $item_id, '_line_tax_data' );

The $tax_data contains the ID and value.