We are now using the transaction ids provided by the banks. This makes things more resilient in terms of duplicate transactions being pushed into YNAB.
However, there is one downside in that because the id format has changed, when running historical imports, we will end up with duplicate transactions for any that were created with the old format.
There is not really a clean way around this, and the only way to fix it is to just delete those duplicate transactions in YNAB. They will only appear once.