If you’re referring to the checkout process, the EU VAT Assistant takes the prefix from the billing country passed to it (note: WooCommerce should be configured to calculate taxes based on customer’s billing or shipping country, not on shop’s base country). The prefix for Belgium is “BE”, the EU VAT Assistant doesn’t change it to “NL”.
My suggestion would be to check if there could be something replacing the billing country passed to the EU VAT Assistant, or altering the VAT number prefix (there’s a filter called wc_aelia_euva_vat_country_prefixes for that purpose).
To help with the troubleshooting, the EU VAT Assistant includes a detailed log, which you can enable by enabling the debug mode in the plugin’s settings. The option is located in the Support tab. With that option enabled, the EU VAT Assistant will write down the data passed to it, such as the country code and the VAT number, as well as the result returned by the validation. That can help you tracing the source of the incorrect country prefix.
If you have a developer who can assist you, they can also review the VAT number validation logic and inspect the data handled by it, by looking into function wp_ajax_validate_eu_vat_number(), which can be found in file plugin-main.php.
If you purchased a support plan for the plugin, we can also investigate the issue for you (such service is not available as part of the free support provided via this forum). In such case, you can contact us via our contact form, at https://aelia.co/contact, and we will send you further instructions.
