WordPress – Custom Field Options Price Update Issue on WooCommerce Variation Change

First, it is better to include the variations warranty prices HTML to the variable product data form. Then you should use WooCommerce variation JS events to change your prices.

Try the following revised code:

// Add variation warranty prices html to the variable product data form
add_action( 'woocommerce_available_variation', 'add_variation_custom_warranty_prices_html', 10, 3 );
function add_variation_custom_warranty_prices_html( $variation_data, $product, $variation ) {
    $display_price         = (float) $variation_data['display_price'];
    $display_regular_price = (float) $variation_data['display_regular_price'];

    // Variation is on sale
    if ( $display_price !== $display_regular_price ) {
        $variation_data['warranty_prices'] = array(
            'no'            => wc_format_sale_price($display_regular_price * 0.9, $display_price * 0.9),
            '1-6months'     => wc_format_sale_price($display_regular_price * 0.92, $display_price * 0.92),
            'over6months'   => wc_format_sale_price($display_regular_price * 0.95, $display_price * 0.95),
            'inactivated'   => wc_format_sale_price($display_regular_price, $display_price),
        );
    } 
    // Variation is not on sale
    else {
        $variation_data['warranty_prices'] = array(
            'no'            => wc_price($display_price * 0.9),
            '1-6months'     => wc_price($display_price * 0.92),
            'over6months'   => wc_price($display_price * 0.95),
            'inactivated'   => wc_price($display_price),
        );
    }
    return  $variation_data;
}

add_action( 'woocommerce_single_variation', 'add_custom_warranty_options', 5 );
function add_custom_warranty_options() {
    // HTML output
    echo '<div class="custom-options-wrapper" style="width: 100%;">
        <h4>'. esc_html__("Great, let's talk about the more details:") . '</h4>
        <div class="custom-warranty-option" style="margin-bottom: 20px;">
            <label>'. esc_html__("1. Is it still under warranty?") . '</label>
            <label style="display: block;">
                <input type="radio" name="warranty_status" value="no" required> '. esc_html__("No, the warranty has expired.") . '
            </label>
            <label style="display: block;">
                <input type="radio" name="warranty_status" value="1-6months" required> '. esc_html__("Yes, 1-6 months warranty") . '
            </label>
            <label style="display: block;">
                <input type="radio" name="warranty_status" value="over6months" required> '. esc_html__("Yes, over 6 months warranty") . '
            </label>
            <label style="display: block;">
                <input type="radio" name="warranty_status" value="inactivated" required> '. esc_html__("Yes, 1 year warranty & inactivated") . '
            </label>
        </div>
    </div>';

    // Enqueued Javascript (jQuery ready event is included)
    wc_enqueue_js( "var warrantyPrices = undefined, selectedWarranty = undefined;
    function updateVariationPriceHtml( warrantyPrices, selectedWarranty ) {
        $.each( warrantyPrices, function( warrantyOption, priceHtml ){
            if( warrantyPrices === undefined || selectedWarranty === undefined ) {
                return false;
            }
            if ( selectedWarranty === warrantyOption ) {
                $('.woocommerce-variation-price > .price').html(priceHtml);
            }
        });
    }

    $('form.variations_form').on('show_variation', function(event, data){ 
        warrantyPrices = data.warranty_prices;
        updateVariationPriceHtml( warrantyPrices, selectedWarranty );
    }).on('hide_variation', function() {
        warrantyPrices = selectedWarranty = undefined;
        $('input[name=warranty_status]').prop('checked', false);
    }).on('change', 'input[name=warranty_status]', function(){
        selectedWarranty = $(this).val();
        updateVariationPriceHtml( warrantyPrices, selectedWarranty );
    });" );
}

Code goes in functions.php file of your child theme (or in a plugin).

Now it will work without any issue.

Addition:

Reset the Warranty selected option on selected variation change

To reset the Warranty selected option on selected variation change, you can change the JavaScript code block inside the 2nd function like:

    // Enqueued Javascript (jQuery ready event is included)
    wc_enqueue_js( "var warrantyPrices = undefined, selectedWarranty = undefined;
    $('form.variations_form').on('show_variation', function(event, data){ 
        warrantyPrices = data.warranty_prices;
        selectedWarranty = undefined;
        $('input[name=warranty_status]').prop('checked', false);
    }).on('hide_variation', function() {   
        warrantyPrices = selectedWarranty = undefined;
        $('input[name=warranty_status]').prop('checked', false);
    }).on('change', 'input[name=warranty_status]', function(){
        selectedWarranty = $(this).val();
        $.each( warrantyPrices, function( warrantyOption, priceHtml ){
            if( warrantyPrices === undefined || selectedWarranty === undefined ) {
                return false;
            }
            if ( selectedWarranty === warrantyOption ) {
                $('.woocommerce-variation-price > .price').html(priceHtml);
            }
        });
    });" );