When entering an invoice with a go cardless the invoice itself is recorded as paid when the mandate is still pending so if the mandate is cancelled on the GoCardless side, the Kashflow invoices will still sat paid.
When setting the invoice and the gocarless mandate, the invoice should not say paid. It should still be unpaid until the money is received.
We also find this to be an annoyance, as you then have to change the date the invoice was paid, manually.