But it does matter if your non Halal / Kosher ingredients ended up in the Halal or Kosher product right?
Yes, but then the implication is to do a mass balance of everything that
isn't Halal/Kosher. Hundreds, if not thousands of raw materials and products... We do a stock check once a year that takes a week; there is no way I will convince it needs to be done twice a year. It is the "mass balance" idea that I struggle with as it makes little sense in our situation and as long as we have hygeine and traceability in place there is nothing that can be said to doubt we meet requirements.
I have just dug out the F0 FAQs Issue 6 V2 and see they have written quite a bit about this, which I think reflects it was badly worded and is causing confusion. Anyway, it seems to imply it just needs to be an audit test sample "for a batch of incoming raw material" so if I roll that into our traceability schedule (we do a test once a month on a raw material, product, process aid or packaging item), hopefully that will do. However, I will do the trace on a product rather than a raw material and have to argue the toss that this makes most sense for us i.e. to show every ingredient in the product is correct.