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Hi @resultancy,
You can use the Attach to setting, under WooCommerce > PDF Invoices > Documents > Invoice, to control in which WooCommerce email notification is the invoice attached.
My recommendation is to select here only the email notifications that are sent when the order is paid, by default Processing or Completed, since before attaching the invoice, it’s created and add a new invoice number to your sequence. However, if you’re receiving an invoice, using the New order email notification, the invoice will be created as soon as the order is placed, so this would not be very important.
Hope it makes sense!