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This thread is resolved. Here is a description of the problem and solution.
How to translate custom WooCommerce email templates.
1. Create the custom email template in WooCommerce.
2. Go to WPML -> Theme and plugins localization and rescan the WooCommerce plugins for strings.
3. Use the 'Strings in admin screens' section of the String Translation to find the email custom text.
4. Move the strings to the String Translation section.
5. Translate the strings and save the translation.