Stock Amazon holds
Half your catalogue may be deliberately left alone.
We always send your WooCommerce count to Amazon, whatever fulfilment method a listing uses. The return leg is where the split is: we only take changes back from Amazon for the items you pick, pack and post yourself. Anything Amazon stores and ships keeps the count Amazon has, and we leave it alone.
That’s a decision rather than a gap. Amazon’s warehouse knows what is on its own shelves and your WooCommerce site doesn’t, so writing a WooCommerce figure over an FBA count would replace a true number with a guess. Where one SKU is sold both ways, the merchant-fulfilled part is the half that tracks your site.
So the question to answer before you switch anything on is which of your listings Amazon fulfils. It decides which way each one moves, and it’s the thing people most often assume rather than check.