Just a quick sample to demonstrate how you could approach asking "Are you sure" when saving a payment

Warn when saving any EDD payment

function custom_prefix_warn_about_old_refunds_js() {

	if ( ! isset( $_GET['prevent_accidental_refunds_js'] ) ) {
		return false;
	}

	header('Content-Type: application/javascript');

	?>

	jQuery( document ).on( 'click', '.edd-order-update-box', function() {
		return(
			confirm('Are you sure you want to do this?')
		);
	} );

	<?php
	die();

}
add_action( 'init', 'custom_prefix_warn_about_old_refunds_js' );


function custom_prefix_enqueue_warn_about_old_refunds_js() {

	wp_enqueue_script( 'custom_prefix_prevent_accidental_refunds_js', get_bloginfo( 'wpurl' ) . '/?prevent_accidental_refunds_js', array( 'jquery' ) );

}
add_action( 'admin_enqueue_scripts', 'custom_prefix_enqueue_warn_about_old_refunds_js' );