Unfortunately I can’t reproduce the issue. Could you send me either the full list of your plugins, or try to disable one by one your plugins to see, if one of them interfers with the plugin, and the metabox reappears.
As it is, there is no way for me to further test, what might be the issue.
If you know want, you can try seeing if the metabox action runs, by editing the /plugins/uploads-for-woocommerce/includes/WooCommerce/Order/Zip.php:line 17 before the add_meta_box( 'woouploads-zip-archive'...
add
var_dump(__FILE__);
Then find $hasUploads = false;
and before this add again
var_dump(__FILE__);
As an alternative you would also change the
add_meta_box( 'woouploads-zip-archive', __( 'Upload actions', 'uploads-for-woocommerce' ), [ $this, 'uploads_box' ], 'shop_order', 'side', 'high' );
to this, and see if it has any effect.
add_meta_box( 'woouploads-zip-archive', __( 'Upload actions', 'uploads-for-woocommerce' ), [ $this, 'uploads_box' ], 'shop_order', 'normal', 'default' );