If you look to WC_Emails
constructor function you will see those 2 related code lines:
add_action( 'woocommerce_email_order_details', array( $this, 'order_downloads' ), 10, 4 );
add_action( 'woocommerce_email_order_details', array( $this, 'order_details' ), 10, 4 );
Based on that code, the following hooked function will set the display of the order downloads section after the order details:
add_action( 'woocommerce_email_order_details', 'wc_email_order_details_action_callback', 1 );
function wc_email_order_details_action_callback() {
remove_action( 'woocommerce_email_order_details', array( WC()->mailer, 'order_downloads' ), 10 );
add_action( 'woocommerce_email_order_details', array( WC()->mailer, 'order_downloads' ), 11, 4 );
}
Code goes in function.php file of your active child theme (or active theme). Tested and works.