Well, I got it working for the most part by issuing an $order->save() after all the updates were complete. Still having an issue with one of my own custom fields, but ACF fields seems to be updating now with that call to save.
Same here using Woocommerce 3.0.4, no custom fields are updating, both my own outside of ACF. Anyone found a solution? I don’t see any difference with rollback to 3.0.1 or latest.
